[e40e335] | 1 | #LyX 1.5.0rc2 created this file. For more info see http://www.lyx.org/
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| 3 | \begin_document
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| 4 | \begin_header
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| 5 | \textclass revtex4
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| 6 | \begin_preamble
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| 7 | \usepackage{listings}
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| 8 | \usepackage[]{hyperref}
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| 9 | \end_preamble
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| 10 | \options rmp, superscriptaddress
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| 11 | \language english
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| 26 | \use_amsmath 1
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| 31 | \secnumdepth 3
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| 32 | \tocdepth 3
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| 33 | \paragraph_separation indent
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| 34 | \defskip medskip
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| 35 | \quotes_language english
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| 36 | \papercolumns 1
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| 37 | \papersides 2
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| 38 | \paperpagestyle default
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| 39 | \tracking_changes false
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| 40 | \output_changes false
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| 41 | \author "Jan H. Meinke"
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| 42 | \end_header
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| 43 |
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| 44 | \begin_body
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| 45 |
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| 46 | \begin_layout Title
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| 47 |
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| 48 | \size huge
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| 49 | SMMP v.
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| 50 | 3
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| 51 | \end_layout
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| 52 |
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| 53 | \begin_layout Author
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| 54 | F.
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| 55 | Eisenmenger
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| 56 | \end_layout
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| 57 |
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| 58 | \begin_layout Author Email
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| 59 | eisenmenger@fmp-berlin.de
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| 60 | \end_layout
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| 61 |
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| 62 | \begin_layout Affiliation
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| 63 | Leibniz-Institut f
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| 64 | \begin_inset ERT
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| 65 | status inlined
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| 66 |
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| 67 | \begin_layout Standard
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| 68 |
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| 69 | {
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| 70 | \backslash
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| 71 | "u}
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| 72 | \end_layout
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| 73 |
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| 74 | \end_inset
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| 75 |
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| 76 | r Molekulare Pharmakologie, 13125 Berlin, Germany
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| 77 | \end_layout
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| 78 |
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| 79 | \begin_layout Author
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| 80 | U.H.E.
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| 81 | Hansmann
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| 82 | \end_layout
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| 83 |
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| 84 | \begin_layout Author Email
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| 85 | hansmann@mtu.edu
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| 86 | \end_layout
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| 87 |
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| 88 | \begin_layout Affiliation
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| 89 | Michigan Technological University, Houghton, MI 49931-1291, USA
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| 90 | \end_layout
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| 91 |
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| 92 | \begin_layout Affiliation
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| 93 | Computational Biology and Biophysics, NIC, 52428 J
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| 94 | \begin_inset ERT
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| 95 | status inlined
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| 96 |
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| 97 | \begin_layout Standard
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| 98 |
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| 99 | {
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| 100 | \backslash
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| 101 | "u}
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| 102 | \end_layout
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| 103 |
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| 104 | \end_inset
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| 105 |
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| 106 | lich, Germany
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| 107 | \end_layout
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| 108 |
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| 109 | \begin_layout Author
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| 110 | Sh.
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| 111 | Hayryan
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| 112 | \end_layout
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| 113 |
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| 114 | \begin_layout Author Email
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| 115 | shura@phys.sinica.edu.tw
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| 116 | \end_layout
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| 117 |
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| 118 | \begin_layout Author
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| 119 | C.-K.
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| 120 | Hu
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| 121 | \end_layout
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| 122 |
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| 123 | \begin_layout Author Email
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| 124 | huck@phys.sinica.edu.tw
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| 125 | \end_layout
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| 126 |
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| 127 | \begin_layout Affiliation
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| 128 | Institute of Physics, Academia Sinica, Nankang, Taipei 11529, Taiwan
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| 129 | \end_layout
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| 130 |
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| 131 | \begin_layout Author
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| 132 | J.
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| 133 | H.
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| 134 | Meinke
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| 135 | \end_layout
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| 136 |
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| 137 | \begin_layout Author Email
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| 138 | j.meinke@fz-juelich.de
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| 139 | \end_layout
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| 140 |
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| 141 | \begin_layout Affiliation
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| 142 | Computational Biology and Biophysics, NIC, 52428 J
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| 143 | \begin_inset ERT
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| 144 | status inlined
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| 145 |
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| 146 | \begin_layout Standard
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| 147 |
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| 148 | {
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| 149 | \backslash
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| 150 | "u}
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| 151 | \end_layout
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| 152 |
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| 153 | \end_inset
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| 154 |
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| 155 | lich, Germany
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| 156 | \end_layout
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| 157 |
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| 158 | \begin_layout Author
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| 159 | S.
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| 160 | Mohanty
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| 161 | \end_layout
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| 162 |
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| 163 | \begin_layout Author Email
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| 164 | s.mohanty@fz-juelich.de
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| 165 | \end_layout
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| 166 |
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| 167 | \begin_layout Affiliation
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| 168 | Computational Biology and Biophysics, NIC, 52428 J
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| 169 | \begin_inset ERT
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| 170 | status inlined
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| 171 |
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| 172 | \begin_layout Standard
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| 173 |
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| 174 | {
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| 175 | \backslash
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| 176 | "u}
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| 177 | \end_layout
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| 178 |
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| 179 | \end_inset
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| 180 |
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| 181 | lich, Germany
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| 182 | \end_layout
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| 183 |
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| 184 | \begin_layout Standard
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| 185 | \noindent
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| 186 | \begin_inset LatexCommand tableofcontents
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| 187 |
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| 188 | \end_inset
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| 189 |
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| 190 |
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| 191 | \end_layout
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| 192 |
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| 193 | \begin_layout Section
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| 194 | Introduction
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| 195 | \end_layout
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| 196 |
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| 197 | \begin_layout Standard
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| 198 | The SMMP (
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| 199 | \series bold
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| 200 | S
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| 201 | \series default
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| 202 | imple
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| 203 | \series bold
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| 204 | M
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| 205 | \series default
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| 206 | olecular
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| 207 | \series bold
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| 208 | M
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| 209 | \series default
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| 210 | echanics for
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| 211 | \series bold
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| 212 | P
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| 213 | \series default
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| 214 | roteins) package is designed for molecular simulations of linear proteins
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| 215 | within the standard geometry model.
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| 216 | The package contains various modern Monte Carlo algorithms and energy minimizat
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| 217 | ion routines.
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| 218 | The energy of a protein can be calculated by exploiting one of four force
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| 219 | fields: ECEPP/2, ECEPP/3
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| 220 | \begin_inset LatexCommand citep
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| 221 | key "ECEPP3"
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| 222 |
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| 223 | \end_inset
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| 224 |
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| 225 | , FLEX or Lund.
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| 226 | Two subroutines for approximating protein-solvent interactions by means
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| 227 | of calculating the solvent accessible surface area of atomic groups are
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| 228 | included.
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| 229 | Nine sets of solvation parameters are available.
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| 230 | All calculations are done with double precision, but the user can easily
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| 231 | modify this option by changing the corresponding IMPLICIT statement.
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| 232 | \end_layout
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| 233 |
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| 234 | \begin_layout Standard
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| 235 | This manual provides the user with the necessary information for installation
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| 236 | of the program, the format of the input and output files, a brief description
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| 237 | of the important routines, and describes some limitations of the package.
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| 238 | A few example runs providing detailed explanation of input and output are
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| 239 | added.
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| 240 | More information on SMMP, definitions, background and references for force
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| 241 | fields and algorithms as used in the program package can be found in
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| 242 | \begin_inset LatexCommand citep
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| 243 | key "Eisenmenger2001,Eisenmenger2006"
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| 244 |
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| 245 | \end_inset
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| 246 |
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| 247 | .
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| 248 | \end_layout
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| 249 |
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| 250 | \begin_layout Standard
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| 251 | SMMP is offered as Open Source.
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| 252 | The program is written in standard FORTRAN.
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| 253 | We encourage users to improve the code and add their own modules.
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| 254 | Please send us your modifications and additions, so we can add them to
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| 255 | future releases.
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| 256 | Or send us a note and let us know where users can download your modules.
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| 257 | The usage and distribution of the program are governed by the following
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| 258 | license agreement:
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| 259 | \newline
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| 260 |
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| 261 | \end_layout
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| 262 |
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| 263 | \begin_layout Quote
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| 264 | SMMP is free software; it can be used, modified, and redistributed under
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| 265 | the terms of the GNU General Public License version 2 (
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| 266 | \shape italic
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| 267 | http://www.gnu.org/licenses/gpl.html
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| 268 | \shape default
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| 269 | ) as published by the Free Software Foundation, EXCEPT WHERE RESTRICTED
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| 270 | BY ONE OF THE FOLLOWING CLAUSES.
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| 271 |
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| 272 | \newline
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| 273 | SMMP shall not be used for commercial or military purposes.
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| 274 | The authors request notification if parts of SMMP are incorporated in other
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| 275 | programs.
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| 276 | \newline
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| 277 | The use of SMMP has to be acknowledged in all resulting publications
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| 278 | by quoting:
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| 279 | \shape italic
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| 280 | F.
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| 281 | Eisenmenger, U.H.E.
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| 282 | Hansmann, S.
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| 283 | Hayryan and C.K.
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| 284 | Hu,
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| 285 | \shape default
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| 286 |
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| 287 | \series bold
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| 288 | [SMMP] A Modern Package for Protein Simulations
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| 289 | \series default
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| 290 | ,
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| 291 | \shape italic
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| 292 | Comp.
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| 293 | Phys.
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| 294 | Comm.
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| 295 | 138 (2001) 192-212
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| 296 | \shape default
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| 297 | ;
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| 298 | \series bold
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| 299 | An Enhanced Version of SMMP - Open-Source Software Package for Simulation
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| 300 | of Proteins
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| 301 | \series default
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| 302 | ,
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| 303 | \shape italic
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| 304 | Comp.
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| 305 | Phys.
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| 306 | Comm.
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| 307 | 174 (2006) 422-
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| 308 | \shape default
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| 309 | 429.
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| 310 |
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| 311 | \emph on
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| 312 | J.
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| 313 | H.
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| 314 | Meinke, S.
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| 315 | Mohanty, F.
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| 316 | Eisenmenger and U.H.E.
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| 317 | Hansmann,
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| 318 | \series bold
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| 319 | \emph default
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| 320 | SMMP v.
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| 321 | 3.0 --- Simulating proteins and protein interactions in Python and Fortran
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| 322 | \series default
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| 323 | , submitted to
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| 324 | \emph on
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| 325 | Comp.\InsetSpace ~
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| 326 | Phys.\InsetSpace ~
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| 327 | Comm.
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| 328 | \emph default
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| 329 |
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| 330 | \newline
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| 331 | SMMP is distributed in the hope that it will be useful, but WITHOUT ANY
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| 332 | WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
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| 333 | FOR A PARTICULAR PURPOSE.
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| 334 | See the GNU General Public License for more details.
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| 335 |
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| 336 | \end_layout
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| 337 |
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| 338 | \begin_layout Standard
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| 339 | \noindent
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| 340 | The most recent version of SMMP can be found on the program package's web
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| 341 | sites:
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| 342 | \series bold
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| 343 | http://www.smmp05.net
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| 344 | \series default
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| 345 | or
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| 346 | \series bold
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| 347 | http://www.phy.mtu.edu/biophys/smmp.htm
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| 348 | \series default
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| 349 | .
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| 350 | Any suggestions for improvements of the code or reports on bugs are welcome.
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| 351 | Please send your remarks to the authors.
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| 352 | \end_layout
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| 353 |
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| 354 | \begin_layout Standard
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| 355 | \noindent
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| 356 |
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| 357 | \series bold
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| 358 | Acknowledgments:
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| 359 | \series default
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| 360 |
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| 361 | \newline
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| 362 | U.H.
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| 363 | acknowledges support by a research grant (CHE-9981874) of the National
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| 364 | Science Foundation (USA).
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| 365 | S.H.
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| 366 | and C.K.H.
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| 367 | are supported by Academia Sinica (Taipei) and by the National Science Council
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| 368 | of the Republic of China (Taiwan) under Contract No.
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| 369 | NSC 89-2112-M-001-084.
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| 370 |
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| 371 | \begin_inset ERT
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| 372 | status collapsed
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| 373 |
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| 374 | \begin_layout Standard
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| 375 |
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| 376 |
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| 377 | \backslash
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| 378 | newpage
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| 379 | \end_layout
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| 380 |
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| 381 | \begin_layout Standard
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| 382 |
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| 383 | \end_layout
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| 384 |
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| 385 | \end_inset
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| 386 |
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| 387 |
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| 388 | \end_layout
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| 389 |
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| 390 | \begin_layout Section
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| 391 | Changes from Previous Version
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| 392 | \end_layout
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| 393 |
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| 394 | \begin_layout Subsection
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| 395 | New Features
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| 396 | \end_layout
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| 397 |
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| 398 | \begin_layout Subsubsection
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| 399 | New Force Field
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| 400 | \end_layout
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| 401 |
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| 402 | \begin_layout Paragraph
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| 403 | Lund Force Field
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| 404 | \end_layout
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| 405 |
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| 406 | \begin_layout Standard
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| 407 | The Lund force fields is a fast force field that uses a minimal set of parameter
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| 408 | s to obtain good folding statistics.
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| 409 | It has been used successfully for protein folding, unfolding, and aggregation
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| 410 | simulations.
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| 411 | For details see
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| 412 | \begin_inset LatexCommand citep
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| 413 | key "Irback2005"
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| 414 |
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| 415 | \end_inset
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| 416 |
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| 417 | .
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| 418 | \end_layout
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| 419 |
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| 420 | \begin_layout Subsubsection
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| 421 | Multi-molecule simulations
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| 422 | \end_layout
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| 423 |
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| 424 | \begin_layout Standard
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| 425 | SMMP 3.0 implements inter-molecular interactions based on the ECEPP/3 force
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| 426 | field.
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| 427 | \end_layout
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| 428 |
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| 429 | \begin_layout Subsubsection
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| 430 | Biased Gaussian Step
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| 431 | \end_layout
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| 432 |
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| 433 | \begin_layout Standard
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| 434 | A new Monte Carlo move that interpolates smoothly between two nearly fixed
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| 435 | end points.
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| 436 | \end_layout
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| 437 |
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| 438 | \begin_layout Subsubsection
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| 439 | Parallel energy calculation
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| 440 | \end_layout
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| 441 |
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| 442 | \begin_layout Standard
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| 443 | The energy calculation for the ECEPP/3 force field can now be done in parallel
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| 444 | making it possible to speed up simulations for serial algorithms.
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| 445 | Combining the parallel energy calculation with parallel tempering, SMMP
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| 446 | can be used efficiently on 2048 processors on an IBM BlueGene/L super computer.
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| 447 | \end_layout
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| 448 |
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| 449 | \begin_layout Subsubsection
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| 450 | Python bindings
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| 451 | \end_layout
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| 452 |
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| 453 | \begin_layout Standard
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| 454 | We now provide Python bindings to SMMP that make the data structure and
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| 455 | algorithms available from (interactive) Python scripts.
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| 456 |
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| 457 | \end_layout
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| 458 |
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| 459 | \begin_layout Subsection
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| 460 | API Changes
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| 461 | \end_layout
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| 462 |
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| 463 | \begin_layout Standard
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| 464 | In previous versions of SMMP the parameters for each algorithm were given
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| 465 | in the source code of the algorithm using PARAMETER statements.
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| 466 | Now, the parameters are passed as function arguments making the program
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| 467 | much more flexible.
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| 468 | The following functions and subroutines now have a different signature:
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| 469 | anneal, canon, minim, mulcan_par, mulcan_sim, outpdb, outvar, partem_p,
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| 470 | and regul.
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| 471 | For details see Section\InsetSpace ~
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| 472 |
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| 473 | \begin_inset LatexCommand ref
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| 474 | reference "sec:Frequently-used-Functions"
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| 475 |
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| 476 | \end_inset
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| 477 |
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| 478 | .
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| 479 |
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| 480 | \end_layout
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| 481 |
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| 482 | \begin_layout Section
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| 483 | Installation
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| 484 | \end_layout
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| 485 |
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| 486 | \begin_layout Standard
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| 487 | SMMP requires a FORTRAN 90 compatbile compiler.
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| 488 | We have compiled it using gfortran, pgif, xlf, and ifort on various platforms.
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| 489 | It should compile and link on any platform with a contemporary FORTRAN
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| 490 | compiler.
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| 491 | All subroutines are stored in *.f or *.f90 files.An example Makefile is included
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| 492 | in the package.
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| 493 | There are no machine dependent routines included in SMMP.
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| 494 | All COMMON blocks and the limiting parameters are gathered in INCL.H, which
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| 495 | is attached to the necessary modules through an INCLUDE statement.
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| 496 | After uncompressing and unpacking (via 'tar -xvf' command) the SMMP package
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| 497 | into a separate directory For the installation of SMMP the user needs to
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| 498 | run
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| 499 | \family typewriter
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| 500 | make
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| 501 | \family default
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| 502 | in the directory with the source code.
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| 503 | You should edit the Makefile to customize the compiler command and compiler
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| 504 | options used.
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| 505 |
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| 506 | \end_layout
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| 507 |
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| 508 | \begin_layout Subsection
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| 509 | Building pySMMP
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| 510 | \end_layout
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| 511 |
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| 512 | \begin_layout Standard
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---|
| 513 | This version of SMMP includes Python bindings to SMMP.
|
---|
| 514 | To build them, you need f2py, which is part of the numpy package.
|
---|
| 515 | If f2py is already installed on your system, pySMMP is built by issuing
|
---|
| 516 | the command
|
---|
| 517 | \emph on
|
---|
| 518 | make pybind
|
---|
| 519 | \emph default
|
---|
| 520 | .
|
---|
| 521 |
|
---|
| 522 | \end_layout
|
---|
| 523 |
|
---|
| 524 | \begin_layout Standard
|
---|
| 525 | \begin_inset ERT
|
---|
| 526 | status collapsed
|
---|
| 527 |
|
---|
| 528 | \begin_layout Standard
|
---|
| 529 |
|
---|
| 530 |
|
---|
| 531 | \backslash
|
---|
| 532 | newpage
|
---|
| 533 | \end_layout
|
---|
| 534 |
|
---|
| 535 | \begin_layout Standard
|
---|
| 536 |
|
---|
| 537 | \end_layout
|
---|
| 538 |
|
---|
| 539 | \begin_layout Standard
|
---|
| 540 |
|
---|
| 541 | \end_layout
|
---|
| 542 |
|
---|
| 543 | \end_inset
|
---|
| 544 |
|
---|
| 545 |
|
---|
| 546 | \end_layout
|
---|
| 547 |
|
---|
| 548 | \begin_layout Section
|
---|
| 549 |
|
---|
| 550 | \emph on
|
---|
| 551 | \noun on
|
---|
| 552 | Biased Gaussian Steps
|
---|
| 553 | \end_layout
|
---|
| 554 |
|
---|
| 555 | \begin_layout Subsection
|
---|
| 556 | Introduction
|
---|
| 557 | \end_layout
|
---|
| 558 |
|
---|
| 559 | \begin_layout Standard
|
---|
| 560 | The Bias Gaussian Step, BGS for short, is a semi-local conformational update,
|
---|
| 561 | involving a concerted rotation of the backbone angles of 4 consecutive
|
---|
| 562 | residues in the protein chain.
|
---|
| 563 | The upstream part of the protein backbone,
|
---|
| 564 | \begin_inset Quotes eld
|
---|
| 565 | \end_inset
|
---|
| 566 |
|
---|
| 567 | before
|
---|
| 568 | \begin_inset Quotes erd
|
---|
| 569 | \end_inset
|
---|
| 570 |
|
---|
| 571 | the first of the 4 residues used for BGS is left unchanged.
|
---|
| 572 | The downstream part,
|
---|
| 573 | \begin_inset Quotes eld
|
---|
| 574 | \end_inset
|
---|
| 575 |
|
---|
| 576 | after
|
---|
| 577 | \begin_inset Quotes erd
|
---|
| 578 | \end_inset
|
---|
| 579 |
|
---|
| 580 | those 4 residues is moved slightly as a rigid body.
|
---|
| 581 | The section containing the 4 BGS residues is locally deformed.
|
---|
| 582 |
|
---|
| 583 | \end_layout
|
---|
| 584 |
|
---|
| 585 | \begin_layout Subsection
|
---|
| 586 | Parameters
|
---|
| 587 | \end_layout
|
---|
| 588 |
|
---|
| 589 | \begin_layout Standard
|
---|
| 590 | The increments to the backbone angles involved in the update are first chosen
|
---|
| 591 | from a Gaussian distribution, and then biased to impart minimal changes
|
---|
| 592 | to the downstream parts of the chain.
|
---|
| 593 | If this later
|
---|
| 594 | \begin_inset Quotes eld
|
---|
| 595 | \end_inset
|
---|
| 596 |
|
---|
| 597 | locality
|
---|
| 598 | \begin_inset Quotes erd
|
---|
| 599 | \end_inset
|
---|
| 600 |
|
---|
| 601 | condition is relaxed, they would be trivially Gaussian-distributed.
|
---|
| 602 | There are two parameters of relevance, called
|
---|
| 603 | \begin_inset ERT
|
---|
| 604 | status open
|
---|
| 605 |
|
---|
| 606 | \begin_layout Standard
|
---|
| 607 |
|
---|
| 608 | $a_{
|
---|
| 609 | \backslash
|
---|
| 610 | mathrm{BGS}}$
|
---|
| 611 | \end_layout
|
---|
| 612 |
|
---|
| 613 | \end_inset
|
---|
| 614 |
|
---|
| 615 | and
|
---|
| 616 | \begin_inset ERT
|
---|
| 617 | status open
|
---|
| 618 |
|
---|
| 619 | \begin_layout Standard
|
---|
| 620 |
|
---|
| 621 | $b_{
|
---|
| 622 | \backslash
|
---|
| 623 | mathrm{BGS}}$
|
---|
| 624 | \end_layout
|
---|
| 625 |
|
---|
| 626 | \end_inset
|
---|
| 627 |
|
---|
| 628 | , declared in the common block
|
---|
| 629 | \noun on
|
---|
| 630 | bgs_r
|
---|
| 631 | \noun default
|
---|
| 632 | .
|
---|
| 633 |
|
---|
| 634 | \begin_inset ERT
|
---|
| 635 | status open
|
---|
| 636 |
|
---|
| 637 | \begin_layout Standard
|
---|
| 638 |
|
---|
| 639 | $a_{
|
---|
| 640 | \backslash
|
---|
| 641 | mathrm{BGS}}$
|
---|
| 642 | \end_layout
|
---|
| 643 |
|
---|
| 644 | \end_inset
|
---|
| 645 |
|
---|
| 646 | controls the size of the increments, and hence directly influences the
|
---|
| 647 | acceptance rate of the updates.
|
---|
| 648 | Smaller the value of
|
---|
| 649 | \begin_inset ERT
|
---|
| 650 | status open
|
---|
| 651 |
|
---|
| 652 | \begin_layout Standard
|
---|
| 653 |
|
---|
| 654 | $a_{
|
---|
| 655 | \backslash
|
---|
| 656 | mathrm{BGS}}$
|
---|
| 657 | \end_layout
|
---|
| 658 |
|
---|
| 659 | \end_inset
|
---|
| 660 |
|
---|
| 661 | , smaller the increments, and hence greater the chances of the update being
|
---|
| 662 | accepted.
|
---|
| 663 | Since a trivial zero size update is of little practical interest, even
|
---|
| 664 | if it is always accepted, it is desirable to have the value of
|
---|
| 665 | \begin_inset ERT
|
---|
| 666 | status open
|
---|
| 667 |
|
---|
| 668 | \begin_layout Standard
|
---|
| 669 |
|
---|
| 670 | $a_{
|
---|
| 671 | \backslash
|
---|
| 672 | mathrm{BGS}}$
|
---|
| 673 | \end_layout
|
---|
| 674 |
|
---|
| 675 | \end_inset
|
---|
| 676 |
|
---|
| 677 | as large as possible.
|
---|
| 678 |
|
---|
| 679 | \begin_inset ERT
|
---|
| 680 | status open
|
---|
| 681 |
|
---|
| 682 | \begin_layout Standard
|
---|
| 683 |
|
---|
| 684 | $b_{
|
---|
| 685 | \backslash
|
---|
| 686 | mathrm{BGS}}$
|
---|
| 687 | \end_layout
|
---|
| 688 |
|
---|
| 689 | \end_inset
|
---|
| 690 |
|
---|
| 691 | controls the degree of locality of the update, i.e., to what extent the downstrea
|
---|
| 692 | m parts should be allowed to move.
|
---|
| 693 | Larger
|
---|
| 694 | \begin_inset ERT
|
---|
| 695 | status open
|
---|
| 696 |
|
---|
| 697 | \begin_layout Standard
|
---|
| 698 |
|
---|
| 699 | $b_{
|
---|
| 700 | \backslash
|
---|
| 701 | mathrm{BGS}}$
|
---|
| 702 | \end_layout
|
---|
| 703 |
|
---|
| 704 | \end_inset
|
---|
| 705 |
|
---|
| 706 | means a stricter locality criterion, and smaller acceptance.
|
---|
| 707 | These two parameters should not be arbitrarily changed.
|
---|
| 708 | The default values in SMMP,
|
---|
| 709 | \begin_inset ERT
|
---|
| 710 | status open
|
---|
| 711 |
|
---|
| 712 | \begin_layout Standard
|
---|
| 713 |
|
---|
| 714 | $a_{
|
---|
| 715 | \backslash
|
---|
| 716 | mathrm{BGS}}=300$
|
---|
| 717 | \end_layout
|
---|
| 718 |
|
---|
| 719 | \end_inset
|
---|
| 720 |
|
---|
| 721 | and
|
---|
| 722 | \begin_inset ERT
|
---|
| 723 | status open
|
---|
| 724 |
|
---|
| 725 | \begin_layout Standard
|
---|
| 726 |
|
---|
| 727 | $b_{
|
---|
| 728 | \backslash
|
---|
| 729 | mathrm{BGS}}=10$
|
---|
| 730 | \end_layout
|
---|
| 731 |
|
---|
| 732 | \end_inset
|
---|
| 733 |
|
---|
| 734 | are tuned, to ensure maximum acceptance at a reasonable update size and
|
---|
| 735 | locality constraint.
|
---|
| 736 |
|
---|
| 737 | \end_layout
|
---|
| 738 |
|
---|
| 739 | \begin_layout Subsection
|
---|
| 740 | Detailed balance and BGS
|
---|
| 741 | \end_layout
|
---|
| 742 |
|
---|
| 743 | \begin_layout Standard
|
---|
| 744 | Information about the current state of the protein is used inside BGS to
|
---|
| 745 | bias the increments towards greater locality.
|
---|
| 746 | Thus the current conformation affects the distribution of the incremental
|
---|
| 747 | angles.
|
---|
| 748 | This means that the reverse update would have a different probability of
|
---|
| 749 | being proposed.
|
---|
| 750 | Because of this, in order to ensure detail balance, an extra multiplicative
|
---|
| 751 | weight factor is needed for BGS along with the standard Metropolis weight,
|
---|
| 752 | to decide whether an update should be accepted.
|
---|
| 753 | The implementation of BGS in SMMP calculates this weight and evaluates
|
---|
| 754 | whether or not the proposed update was accepted.
|
---|
| 755 |
|
---|
| 756 | \end_layout
|
---|
| 757 |
|
---|
| 758 | \begin_layout Subsection
|
---|
| 759 | The function BGS in SMMP
|
---|
| 760 | \end_layout
|
---|
| 761 |
|
---|
| 762 | \begin_layout Standard
|
---|
| 763 | BGS is implemented in SMMP as a function with the following signature:
|
---|
| 764 | \end_layout
|
---|
| 765 |
|
---|
| 766 | \begin_layout Standard
|
---|
| 767 | integer function bgs(eol1,dummy)
|
---|
| 768 | \end_layout
|
---|
| 769 |
|
---|
| 770 | \begin_layout Standard
|
---|
| 771 | The parameter eol1 passed to BGS is the energy of the system before the
|
---|
| 772 | call.
|
---|
| 773 | The argument
|
---|
| 774 | \begin_inset Quotes eld
|
---|
| 775 | \end_inset
|
---|
| 776 |
|
---|
| 777 | dummy
|
---|
| 778 | \begin_inset Quotes erd
|
---|
| 779 | \end_inset
|
---|
| 780 |
|
---|
| 781 | is a function that calculates the exponent of the Metropolis weight function.
|
---|
| 782 | The return value is 1 for an accepted BGS move and 0 for a rejected move.
|
---|
| 783 |
|
---|
| 784 | \end_layout
|
---|
| 785 |
|
---|
| 786 | \begin_layout Subsubsection
|
---|
| 787 | Using BGS in SMMP
|
---|
| 788 | \end_layout
|
---|
| 789 |
|
---|
| 790 | \begin_layout Standard
|
---|
| 791 | To use BGS, one must ensure that the subroutine init_lund, which initialises
|
---|
| 792 | several arrays used in BGS, is called during the initialisation phase of
|
---|
| 793 | the program.
|
---|
| 794 | These arrays store information about the BGS-capable angles in the protein
|
---|
| 795 | chain.
|
---|
| 796 | Therefore, init_lund should be called again, in case the program changes
|
---|
| 797 | the amino acid sequence of a molecule or the total number of molecules
|
---|
| 798 | in the system.
|
---|
| 799 |
|
---|
| 800 | \end_layout
|
---|
| 801 |
|
---|
| 802 | \begin_layout Standard
|
---|
| 803 | The global switch
|
---|
| 804 | \noun on
|
---|
| 805 | upchswitch
|
---|
| 806 | \noun default
|
---|
| 807 | controls how BGS is used by the metropolis subroutine, which is normally
|
---|
| 808 | the routine that calls BGS.
|
---|
| 809 | For
|
---|
| 810 | \noun on
|
---|
| 811 | upchswitch=0, BGS
|
---|
| 812 | \noun default
|
---|
| 813 | is never used.
|
---|
| 814 | For
|
---|
| 815 | \noun on
|
---|
| 816 | upchswitch=1,
|
---|
| 817 | \noun default
|
---|
| 818 | it is used with a probabilty
|
---|
| 819 | \noun on
|
---|
| 820 | bgsprob
|
---|
| 821 | \noun default
|
---|
| 822 | , which is another global parameter.
|
---|
| 823 | For
|
---|
| 824 | \noun on
|
---|
| 825 | upchswitch=2,
|
---|
| 826 | \noun default
|
---|
| 827 | BGS is used when possible with a temperature dependent probability.
|
---|
| 828 | At higher temperatures abrupt single angle changes are more effective in
|
---|
| 829 | browsing the conformation space quickly.
|
---|
| 830 | A local update like BGS should therefore have a small probability at high
|
---|
| 831 | temperatures.
|
---|
| 832 | At low temperatures, often the system is in a compact state with significant
|
---|
| 833 | secondary structure, and it is desirable to explore the neighbourhood of
|
---|
| 834 | that state to refine the structure.
|
---|
| 835 | BGS is more efficient at this compared to single angle updates, and hence
|
---|
| 836 | should have a higher probability at lower temperatures.
|
---|
| 837 | The choice,
|
---|
| 838 | \noun on
|
---|
| 839 | upchswitch=2
|
---|
| 840 | \noun default
|
---|
| 841 | uses this scheme for BGS use.
|
---|
| 842 |
|
---|
| 843 | \end_layout
|
---|
| 844 |
|
---|
| 845 | \begin_layout Section
|
---|
| 846 | Getting Started
|
---|
| 847 | \end_layout
|
---|
| 848 |
|
---|
| 849 | \begin_layout Standard
|
---|
| 850 | The quickest way to get started is to use one of the examples in the EXAMPLES
|
---|
| 851 | directory as a template.
|
---|
| 852 | The examples are described in Section\InsetSpace ~
|
---|
| 853 |
|
---|
| 854 | \begin_inset LatexCommand ref
|
---|
| 855 | reference "sec:Examples"
|
---|
| 856 |
|
---|
| 857 | \end_inset
|
---|
| 858 |
|
---|
| 859 | .
|
---|
| 860 | \end_layout
|
---|
| 861 |
|
---|
| 862 | \begin_layout Standard
|
---|
| 863 | SMMP does not include an interpretor of user-defined commands instead the
|
---|
| 864 | preparation of a simulation is done in the MAIN module calling corresponding
|
---|
| 865 | simulation subroutine(s).
|
---|
| 866 | After adjusting MAIN to your needs, SMMP has to be re-compiled.
|
---|
| 867 | We provide a sample main file with detailed comments.
|
---|
| 868 | For a comment-free version see Listing
|
---|
| 869 | \begin_inset LatexCommand ref
|
---|
| 870 | reference "listing:mainmc"
|
---|
| 871 |
|
---|
| 872 | \end_inset
|
---|
| 873 |
|
---|
| 874 | .
|
---|
| 875 |
|
---|
| 876 | \end_layout
|
---|
| 877 |
|
---|
| 878 | \begin_layout Standard
|
---|
| 879 | \begin_inset listings
|
---|
| 880 | lstparams "float=h,language=Fortran,numbers=left"
|
---|
| 881 | inline false
|
---|
| 882 | status open
|
---|
| 883 |
|
---|
| 884 | \begin_layout Standard
|
---|
| 885 |
|
---|
| 886 | program main
|
---|
| 887 | \end_layout
|
---|
| 888 |
|
---|
| 889 | \begin_layout Standard
|
---|
| 890 |
|
---|
| 891 | include "../INCL.H"
|
---|
| 892 | \end_layout
|
---|
| 893 |
|
---|
| 894 | \begin_layout Standard
|
---|
| 895 |
|
---|
| 896 |
|
---|
| 897 | \end_layout
|
---|
| 898 |
|
---|
| 899 | \begin_layout Standard
|
---|
| 900 |
|
---|
| 901 | character*80 libdir, seqfile, varfile
|
---|
| 902 | \end_layout
|
---|
| 903 |
|
---|
| 904 | \begin_layout Standard
|
---|
| 905 |
|
---|
| 906 | character grpn*4,grpc*4
|
---|
| 907 | \end_layout
|
---|
| 908 |
|
---|
| 909 | \begin_layout Standard
|
---|
| 910 |
|
---|
| 911 | integer nequi, nsweeps, nmes
|
---|
| 912 | \end_layout
|
---|
| 913 |
|
---|
| 914 | \begin_layout Standard
|
---|
| 915 |
|
---|
| 916 | double precision tmax, tmin
|
---|
| 917 | \end_layout
|
---|
| 918 |
|
---|
| 919 | \begin_layout Standard
|
---|
| 920 |
|
---|
| 921 | logical lrand
|
---|
| 922 | \end_layout
|
---|
| 923 |
|
---|
| 924 | \begin_layout Standard
|
---|
| 925 |
|
---|
| 926 | \end_layout
|
---|
| 927 |
|
---|
| 928 | \begin_layout Standard
|
---|
| 929 |
|
---|
| 930 | libdir = '../SMMP/'
|
---|
| 931 | \end_layout
|
---|
| 932 |
|
---|
| 933 | \begin_layout Standard
|
---|
| 934 |
|
---|
| 935 | ientyp = 0
|
---|
| 936 | \end_layout
|
---|
| 937 |
|
---|
| 938 | \begin_layout Standard
|
---|
| 939 |
|
---|
| 940 | sh2 = .true.
|
---|
| 941 |
|
---|
| 942 | \end_layout
|
---|
| 943 |
|
---|
| 944 | \begin_layout Standard
|
---|
| 945 |
|
---|
| 946 | itysol = 0
|
---|
| 947 | \end_layout
|
---|
| 948 |
|
---|
| 949 | \begin_layout Standard
|
---|
| 950 |
|
---|
| 951 | call init_energy(libdir)
|
---|
| 952 | \end_layout
|
---|
| 953 |
|
---|
| 954 | \begin_layout Standard
|
---|
| 955 |
|
---|
| 956 | \end_layout
|
---|
| 957 |
|
---|
| 958 | \begin_layout Standard
|
---|
| 959 |
|
---|
| 960 | grpn = 'nh2'
|
---|
| 961 | \end_layout
|
---|
| 962 |
|
---|
| 963 | \begin_layout Standard
|
---|
| 964 |
|
---|
| 965 | grpc = 'cooh'
|
---|
| 966 | \end_layout
|
---|
| 967 |
|
---|
| 968 | \begin_layout Standard
|
---|
| 969 |
|
---|
| 970 | iabin = 1
|
---|
| 971 | \end_layout
|
---|
| 972 |
|
---|
| 973 | \begin_layout Standard
|
---|
| 974 |
|
---|
| 975 | seqfile='EXAMPLES/enkefa.seq'
|
---|
| 976 | \end_layout
|
---|
| 977 |
|
---|
| 978 | \begin_layout Standard
|
---|
| 979 |
|
---|
| 980 | varfile='EXAMPLES/enkefa.var'
|
---|
| 981 | \end_layout
|
---|
| 982 |
|
---|
| 983 | \begin_layout Standard
|
---|
| 984 |
|
---|
| 985 | ntlml = 0
|
---|
| 986 | \end_layout
|
---|
| 987 |
|
---|
| 988 | \begin_layout Standard
|
---|
| 989 |
|
---|
| 990 | call init_molecule(iabin,grpn,grpc,seqfile,varfile)
|
---|
| 991 | \end_layout
|
---|
| 992 |
|
---|
| 993 | \begin_layout Standard
|
---|
| 994 |
|
---|
| 995 | \end_layout
|
---|
| 996 |
|
---|
| 997 | \begin_layout Standard
|
---|
| 998 |
|
---|
| 999 | seed = 81236
|
---|
| 1000 | \end_layout
|
---|
| 1001 |
|
---|
| 1002 | \begin_layout Standard
|
---|
| 1003 |
|
---|
| 1004 | call sgrnd(seed)
|
---|
| 1005 | \end_layout
|
---|
| 1006 |
|
---|
| 1007 | \begin_layout Standard
|
---|
| 1008 |
|
---|
| 1009 | upchswitch= 0
|
---|
| 1010 | \end_layout
|
---|
| 1011 |
|
---|
| 1012 | \begin_layout Standard
|
---|
| 1013 |
|
---|
| 1014 |
|
---|
| 1015 | \end_layout
|
---|
| 1016 |
|
---|
| 1017 | \begin_layout Standard
|
---|
| 1018 |
|
---|
| 1019 | nequi=100
|
---|
| 1020 | \end_layout
|
---|
| 1021 |
|
---|
| 1022 | \begin_layout Standard
|
---|
| 1023 |
|
---|
| 1024 | nsweeps=100000
|
---|
| 1025 | \end_layout
|
---|
| 1026 |
|
---|
| 1027 | \begin_layout Standard
|
---|
| 1028 |
|
---|
| 1029 | nmes=1000
|
---|
| 1030 | \end_layout
|
---|
| 1031 |
|
---|
| 1032 | \begin_layout Standard
|
---|
| 1033 |
|
---|
| 1034 | temp = 300
|
---|
| 1035 | \end_layout
|
---|
| 1036 |
|
---|
| 1037 | \begin_layout Standard
|
---|
| 1038 |
|
---|
| 1039 | lrand=.true.
|
---|
| 1040 |
|
---|
| 1041 | \end_layout
|
---|
| 1042 |
|
---|
| 1043 | \begin_layout Standard
|
---|
| 1044 |
|
---|
| 1045 | call canon(nequi, nsweeps, nmes, temp,lrand)
|
---|
| 1046 | \end_layout
|
---|
| 1047 |
|
---|
| 1048 | \begin_layout Standard
|
---|
| 1049 |
|
---|
| 1050 |
|
---|
| 1051 | \end_layout
|
---|
| 1052 |
|
---|
| 1053 | \begin_layout Standard
|
---|
| 1054 |
|
---|
| 1055 | end program main
|
---|
| 1056 | \end_layout
|
---|
| 1057 |
|
---|
| 1058 | \begin_layout Standard
|
---|
| 1059 |
|
---|
| 1060 | \begin_inset Caption
|
---|
| 1061 |
|
---|
| 1062 | \begin_layout Standard
|
---|
| 1063 | The basic main function for a Monte Carlo Simulation
|
---|
| 1064 | \begin_inset LatexCommand label
|
---|
| 1065 | name "listing:mainmc"
|
---|
| 1066 |
|
---|
| 1067 | \end_inset
|
---|
| 1068 |
|
---|
| 1069 |
|
---|
| 1070 | \end_layout
|
---|
| 1071 |
|
---|
| 1072 | \end_inset
|
---|
| 1073 |
|
---|
| 1074 |
|
---|
| 1075 | \end_layout
|
---|
| 1076 |
|
---|
| 1077 | \end_inset
|
---|
| 1078 |
|
---|
| 1079 |
|
---|
| 1080 | \end_layout
|
---|
| 1081 |
|
---|
| 1082 | \begin_layout Standard
|
---|
| 1083 | The following steps summarize how to run SMMP:
|
---|
| 1084 | \end_layout
|
---|
| 1085 |
|
---|
| 1086 | \begin_layout Enumerate
|
---|
| 1087 | Assign the path to the directory containing the standard amino acid residue
|
---|
| 1088 | libraries and the file 'charges' to the character variable 'libdir' (Line
|
---|
| 1089 | 10).
|
---|
| 1090 | \end_layout
|
---|
| 1091 |
|
---|
| 1092 | \begin_layout Enumerate
|
---|
| 1093 | Select the force field and solvation model by setting the four paramters
|
---|
| 1094 | 'flex', 'sh2', 'epsd', and 'itysol' to their appropriate values:
|
---|
| 1095 | \begin_inset ERT
|
---|
| 1096 | status open
|
---|
| 1097 |
|
---|
| 1098 | \begin_layout Standard
|
---|
| 1099 |
|
---|
| 1100 |
|
---|
| 1101 | \backslash
|
---|
| 1102 | begin{verbatim}
|
---|
| 1103 | \end_layout
|
---|
| 1104 |
|
---|
| 1105 | \begin_layout Standard
|
---|
| 1106 |
|
---|
| 1107 | * ientyp = 0 : ECEPP
|
---|
| 1108 | \end_layout
|
---|
| 1109 |
|
---|
| 1110 | \begin_layout Standard
|
---|
| 1111 |
|
---|
| 1112 | 1 : FLEX
|
---|
| 1113 | \end_layout
|
---|
| 1114 |
|
---|
| 1115 | \begin_layout Standard
|
---|
| 1116 |
|
---|
| 1117 | 2 : LUND
|
---|
| 1118 | \end_layout
|
---|
| 1119 |
|
---|
| 1120 | \begin_layout Standard
|
---|
| 1121 |
|
---|
| 1122 | 3 : ECEPP + Abagyan
|
---|
| 1123 | \end_layout
|
---|
| 1124 |
|
---|
| 1125 | \begin_layout Standard
|
---|
| 1126 |
|
---|
| 1127 | * sh2 =.TRUE.
|
---|
| 1128 | : ECEPP/2 potential, sh2=.FALSE.: ECEPP/3
|
---|
| 1129 | \end_layout
|
---|
| 1130 |
|
---|
| 1131 | \begin_layout Standard
|
---|
| 1132 |
|
---|
| 1133 | * epsd=.TRUE.
|
---|
| 1134 | : Distant dependent dielectric permittivity
|
---|
| 1135 | \end_layout
|
---|
| 1136 |
|
---|
| 1137 | \begin_layout Standard
|
---|
| 1138 |
|
---|
| 1139 | epsd=.FALSE.
|
---|
| 1140 | : epsilon = 2
|
---|
| 1141 | \end_layout
|
---|
| 1142 |
|
---|
| 1143 | \begin_layout Standard
|
---|
| 1144 |
|
---|
| 1145 | * itysol = 0 : gas phase,
|
---|
| 1146 | \end_layout
|
---|
| 1147 |
|
---|
| 1148 | \begin_layout Standard
|
---|
| 1149 |
|
---|
| 1150 | itysol > 0 : approximation of protein-solvent interactions by means
|
---|
| 1151 | \end_layout
|
---|
| 1152 |
|
---|
| 1153 | \begin_layout Standard
|
---|
| 1154 |
|
---|
| 1155 | of a solvent accessible surface area approach with
|
---|
| 1156 | \end_layout
|
---|
| 1157 |
|
---|
| 1158 | \begin_layout Standard
|
---|
| 1159 |
|
---|
| 1160 | numerical estimation of the accessible area,
|
---|
| 1161 | \end_layout
|
---|
| 1162 |
|
---|
| 1163 | \begin_layout Standard
|
---|
| 1164 |
|
---|
| 1165 | itysol < 0 : same as above, but the accessible area is calculated
|
---|
| 1166 | \end_layout
|
---|
| 1167 |
|
---|
| 1168 | \begin_layout Standard
|
---|
| 1169 |
|
---|
| 1170 | analytically (considerably than itysol > 0).
|
---|
| 1171 | \end_layout
|
---|
| 1172 |
|
---|
| 1173 | \begin_layout Standard
|
---|
| 1174 |
|
---|
| 1175 |
|
---|
| 1176 | \backslash
|
---|
| 1177 | end{verbatim}
|
---|
| 1178 | \end_layout
|
---|
| 1179 |
|
---|
| 1180 | \end_inset
|
---|
| 1181 |
|
---|
| 1182 | (Line 11--13).
|
---|
| 1183 | \end_layout
|
---|
| 1184 |
|
---|
| 1185 | \begin_layout Enumerate
|
---|
| 1186 |
|
---|
| 1187 | \shape italic
|
---|
| 1188 | call init_energy(libdir)
|
---|
| 1189 | \shape default
|
---|
| 1190 | to initialize the energy parametrization (Line 12).
|
---|
| 1191 | \end_layout
|
---|
| 1192 |
|
---|
| 1193 | \begin_layout Enumerate
|
---|
| 1194 | Choose the N-terminal and C-terminal groups by assigning to appropriate
|
---|
| 1195 | strings to variables 'grpn' and 'grpc' (Line 16--17)
|
---|
| 1196 | \end_layout
|
---|
| 1197 |
|
---|
| 1198 | \begin_layout Enumerate
|
---|
| 1199 | Choose how the initial input is read in:
|
---|
| 1200 | \begin_inset ERT
|
---|
| 1201 | status collapsed
|
---|
| 1202 |
|
---|
| 1203 | \begin_layout Standard
|
---|
| 1204 |
|
---|
| 1205 |
|
---|
| 1206 | \backslash
|
---|
| 1207 | begin{verbatim}
|
---|
| 1208 | \end_layout
|
---|
| 1209 |
|
---|
| 1210 | \begin_layout Standard
|
---|
| 1211 |
|
---|
| 1212 | * iabin = 0 : read from PDB-file
|
---|
| 1213 | \end_layout
|
---|
| 1214 |
|
---|
| 1215 | \begin_layout Standard
|
---|
| 1216 |
|
---|
| 1217 | * iabin = 1 : read from sequence (and configuration) file
|
---|
| 1218 | \end_layout
|
---|
| 1219 |
|
---|
| 1220 | \begin_layout Standard
|
---|
| 1221 |
|
---|
| 1222 |
|
---|
| 1223 | \backslash
|
---|
| 1224 | end{verbatim}
|
---|
| 1225 | \end_layout
|
---|
| 1226 |
|
---|
| 1227 | \end_inset
|
---|
| 1228 |
|
---|
| 1229 | (Line 18)
|
---|
| 1230 | \end_layout
|
---|
| 1231 |
|
---|
| 1232 | \begin_layout Enumerate
|
---|
| 1233 | Enter the names of the corresponding file(s) '
|
---|
| 1234 | \shape italic
|
---|
| 1235 | seqfil
|
---|
| 1236 | \shape default
|
---|
| 1237 | ' and '
|
---|
| 1238 | \shape italic
|
---|
| 1239 | varfil
|
---|
| 1240 | \shape default
|
---|
| 1241 | ' (Line 19--20).
|
---|
| 1242 | If there are empty, they'll be requested through an interactive command
|
---|
| 1243 | line dialog, issued by '
|
---|
| 1244 | \shape italic
|
---|
| 1245 | call init_molecule
|
---|
| 1246 | \shape default
|
---|
| 1247 | ' (Line 22).
|
---|
| 1248 | The user can easily just supply the corresponding file names in a "here
|
---|
| 1249 | document", as shown in the example scripts .
|
---|
| 1250 | \end_layout
|
---|
| 1251 |
|
---|
| 1252 | \begin_layout Enumerate
|
---|
| 1253 | At this point the program is ready for calling task subroutines.
|
---|
| 1254 | Here we perform a canonical Monte Carlo simulation at T=300K.
|
---|
| 1255 | Two kinds of updates are avaible: a single angle update and the biased
|
---|
| 1256 | Gaussian step (bgs).
|
---|
| 1257 | For this simulation we turn bgs off by setting
|
---|
| 1258 | \family typewriter
|
---|
| 1259 | upchswitch=0
|
---|
| 1260 | \family default
|
---|
| 1261 | .
|
---|
| 1262 | Detailed examples for this and other simulation tasks can be found in the
|
---|
| 1263 | following section.
|
---|
| 1264 | Normally, simulation subroutines write data in output files, but one can
|
---|
| 1265 | also use output routines such as `
|
---|
| 1266 | \shape italic
|
---|
| 1267 | outpdb
|
---|
| 1268 | \shape default
|
---|
| 1269 | ' in '
|
---|
| 1270 | \shape italic
|
---|
| 1271 | main
|
---|
| 1272 | \shape default
|
---|
| 1273 | '.
|
---|
| 1274 | The minimal output (written into standard output) is the name of the sequence
|
---|
| 1275 | file (extension .seq), name of configuration file (extension .var), and for
|
---|
| 1276 | each residue a list of dihedral angles together with their initially assigned
|
---|
| 1277 | values.
|
---|
| 1278 |
|
---|
| 1279 | \end_layout
|
---|
| 1280 |
|
---|
| 1281 | \begin_layout Enumerate
|
---|
| 1282 | For parallel tempering jobs on on a multiprocessor system one has to replace
|
---|
| 1283 | '
|
---|
| 1284 | \shape italic
|
---|
| 1285 | main
|
---|
| 1286 | \shape default
|
---|
| 1287 | ' by '
|
---|
| 1288 | \shape italic
|
---|
| 1289 | pmain
|
---|
| 1290 | \shape default
|
---|
| 1291 | '.
|
---|
| 1292 | The above protocol still applies, but one has to provide in addition the
|
---|
| 1293 | number of nodes with the variable '
|
---|
| 1294 | \shape italic
|
---|
| 1295 | no
|
---|
| 1296 | \shape default
|
---|
| 1297 | '.
|
---|
| 1298 |
|
---|
| 1299 | \end_layout
|
---|
| 1300 |
|
---|
| 1301 | \begin_layout Section
|
---|
| 1302 | Programming with SMMP
|
---|
| 1303 | \end_layout
|
---|
| 1304 |
|
---|
| 1305 | \begin_layout Standard
|
---|
| 1306 | While SMMP provides several efficient sampling algorithms, you may want
|
---|
| 1307 | to improve an existing or implement a new algorithm.
|
---|
| 1308 | This section goes into more details and explains some of the nuts and bolts
|
---|
| 1309 | of SMMP.
|
---|
| 1310 | \end_layout
|
---|
| 1311 |
|
---|
| 1312 | \begin_layout Paragraph
|
---|
| 1313 | Where can I find information about atoms, residues, proteins, and dihedrals
|
---|
| 1314 | \end_layout
|
---|
| 1315 |
|
---|
| 1316 | \begin_layout Standard
|
---|
| 1317 | Configurations are stored in one dimensional arrays defined in INCL.H and
|
---|
| 1318 | shared through common blocks.
|
---|
| 1319 | \begin_inset Note Note
|
---|
| 1320 | status collapsed
|
---|
| 1321 |
|
---|
| 1322 | \begin_layout Standard
|
---|
| 1323 | I hope, we'll have moved most of the arrays to modules before publication.
|
---|
| 1324 | \end_layout
|
---|
| 1325 |
|
---|
| 1326 | \end_inset
|
---|
| 1327 |
|
---|
| 1328 | It helps to think somewhat object oriented to understand the structure
|
---|
| 1329 | of the arrays.
|
---|
| 1330 | In general integer arrays start with the letter 'i'.
|
---|
| 1331 | The abbreviation 'ml' relates to molecules, 'rs' to residues, and 'at'
|
---|
| 1332 | to atoms.
|
---|
| 1333 | Several boundary arrays are pointers to the first and last element and
|
---|
| 1334 | end in '1' for the first element and '2' for the last element.
|
---|
| 1335 | For example, irsml1(i) is the index of the first residue in molecule
|
---|
| 1336 | \begin_inset Formula $i$
|
---|
| 1337 | \end_inset
|
---|
| 1338 |
|
---|
| 1339 | , iatrs1(irsml(i)) is the index of the first atom of the first residue of
|
---|
| 1340 | molecule
|
---|
| 1341 | \begin_inset Formula $i$
|
---|
| 1342 | \end_inset
|
---|
| 1343 |
|
---|
| 1344 | .
|
---|
| 1345 | If iat = iatrs1(irsml(i)), then we can access the coordinates of the atom
|
---|
| 1346 | using xat(iat), yat(iat), z(iat).
|
---|
| 1347 | Using this scheme we can cycle through all the atoms in the system.
|
---|
| 1348 | An example is shown in Listing
|
---|
| 1349 | \begin_inset ERT
|
---|
| 1350 | status open
|
---|
| 1351 |
|
---|
| 1352 | \begin_layout Standard
|
---|
| 1353 |
|
---|
| 1354 |
|
---|
| 1355 | \backslash
|
---|
| 1356 | ref{listing:outpdb}
|
---|
| 1357 | \end_layout
|
---|
| 1358 |
|
---|
| 1359 | \end_inset
|
---|
| 1360 |
|
---|
| 1361 | .
|
---|
| 1362 |
|
---|
| 1363 | \begin_inset ERT
|
---|
| 1364 | status open
|
---|
| 1365 |
|
---|
| 1366 | \begin_layout Standard
|
---|
| 1367 |
|
---|
| 1368 |
|
---|
| 1369 | \backslash
|
---|
| 1370 | lstset{language=Fortran}
|
---|
| 1371 | \end_layout
|
---|
| 1372 |
|
---|
| 1373 | \begin_layout Standard
|
---|
| 1374 |
|
---|
| 1375 |
|
---|
| 1376 | \backslash
|
---|
| 1377 | begin{lstlisting}[float=p, caption={Using the indices to cycle through all
|
---|
| 1378 | the atoms in the system.
|
---|
| 1379 | This snippet is taken from the subroutine outpdb, which writes the current
|
---|
| 1380 | configuration to a file using the pdb format.}, label=listing:outpdb]
|
---|
| 1381 | \end_layout
|
---|
| 1382 |
|
---|
| 1383 | \begin_layout Standard
|
---|
| 1384 |
|
---|
| 1385 | irs=0
|
---|
| 1386 | \end_layout
|
---|
| 1387 |
|
---|
| 1388 | \begin_layout Standard
|
---|
| 1389 |
|
---|
| 1390 | iat0 = 0
|
---|
| 1391 | \end_layout
|
---|
| 1392 |
|
---|
| 1393 | \begin_layout Standard
|
---|
| 1394 |
|
---|
| 1395 | do inml = nml0, nml1
|
---|
| 1396 | \end_layout
|
---|
| 1397 |
|
---|
| 1398 | \begin_layout Standard
|
---|
| 1399 |
|
---|
| 1400 | iat = iat0
|
---|
| 1401 | \end_layout
|
---|
| 1402 |
|
---|
| 1403 | \begin_layout Standard
|
---|
| 1404 |
|
---|
| 1405 | chid = char(64 + inml)
|
---|
| 1406 | \end_layout
|
---|
| 1407 |
|
---|
| 1408 | \begin_layout Standard
|
---|
| 1409 |
|
---|
| 1410 | ifirs=irsml1(inml)
|
---|
| 1411 | \end_layout
|
---|
| 1412 |
|
---|
| 1413 | \begin_layout Standard
|
---|
| 1414 |
|
---|
| 1415 | ifiat=iatrs1(ifirs)
|
---|
| 1416 | \end_layout
|
---|
| 1417 |
|
---|
| 1418 | \begin_layout Standard
|
---|
| 1419 |
|
---|
| 1420 | do nrs=ifirs,irsml2(inml)
|
---|
| 1421 | \end_layout
|
---|
| 1422 |
|
---|
| 1423 | \begin_layout Standard
|
---|
| 1424 |
|
---|
| 1425 | irs=irs+1
|
---|
| 1426 | \end_layout
|
---|
| 1427 |
|
---|
| 1428 | \begin_layout Standard
|
---|
| 1429 |
|
---|
| 1430 | res(1:)=seq(nrs)(1:3)
|
---|
| 1431 | \end_layout
|
---|
| 1432 |
|
---|
| 1433 | \begin_layout Standard
|
---|
| 1434 |
|
---|
| 1435 | do i=iatrs1(nrs),iatrs2(nrs)
|
---|
| 1436 | \end_layout
|
---|
| 1437 |
|
---|
| 1438 | \begin_layout Standard
|
---|
| 1439 |
|
---|
| 1440 | iat=iat+1
|
---|
| 1441 | \end_layout
|
---|
| 1442 |
|
---|
| 1443 | \begin_layout Standard
|
---|
| 1444 |
|
---|
| 1445 | atnm=' '
|
---|
| 1446 | \end_layout
|
---|
| 1447 |
|
---|
| 1448 | \begin_layout Standard
|
---|
| 1449 |
|
---|
| 1450 | atnm(2:5)=nmat(i) ! nmat(i) contains the name of atom i
|
---|
| 1451 | \end_layout
|
---|
| 1452 |
|
---|
| 1453 | \begin_layout Standard
|
---|
| 1454 |
|
---|
| 1455 | if (atnm(5:5).ne.' ') then
|
---|
| 1456 | \end_layout
|
---|
| 1457 |
|
---|
| 1458 | \begin_layout Standard
|
---|
| 1459 |
|
---|
| 1460 | atnm(1:1)=atnm(5:5) !!
|
---|
| 1461 | \end_layout
|
---|
| 1462 |
|
---|
| 1463 | \begin_layout Standard
|
---|
| 1464 |
|
---|
| 1465 | atnm(5:5)=' '
|
---|
| 1466 | \end_layout
|
---|
| 1467 |
|
---|
| 1468 | \begin_layout Standard
|
---|
| 1469 |
|
---|
| 1470 | endif
|
---|
| 1471 | \end_layout
|
---|
| 1472 |
|
---|
| 1473 | \begin_layout Standard
|
---|
| 1474 |
|
---|
| 1475 | z=zat(i)-rz
|
---|
| 1476 | \end_layout
|
---|
| 1477 |
|
---|
| 1478 | \begin_layout Standard
|
---|
| 1479 |
|
---|
| 1480 | call toupst(atnm) ! converts a string to all uppercase
|
---|
| 1481 | \end_layout
|
---|
| 1482 |
|
---|
| 1483 | \begin_layout Standard
|
---|
| 1484 |
|
---|
| 1485 | call toupst(res)
|
---|
| 1486 | \end_layout
|
---|
| 1487 |
|
---|
| 1488 | \begin_layout Standard
|
---|
| 1489 |
|
---|
| 1490 | \end_layout
|
---|
| 1491 |
|
---|
| 1492 | \begin_layout Standard
|
---|
| 1493 |
|
---|
| 1494 | write (npdb,1) 'ATOM',iat,atnm,res(1:3),chid,irs,cdin,
|
---|
| 1495 | \end_layout
|
---|
| 1496 |
|
---|
| 1497 | \begin_layout Standard
|
---|
| 1498 |
|
---|
| 1499 | xat(i), yat(i),zat(i),occ,bva
|
---|
| 1500 |
|
---|
| 1501 | \end_layout
|
---|
| 1502 |
|
---|
| 1503 | \begin_layout Standard
|
---|
| 1504 |
|
---|
| 1505 | enddo
|
---|
| 1506 | \end_layout
|
---|
| 1507 |
|
---|
| 1508 | \begin_layout Standard
|
---|
| 1509 |
|
---|
| 1510 | enddo
|
---|
| 1511 | \end_layout
|
---|
| 1512 |
|
---|
| 1513 | \begin_layout Standard
|
---|
| 1514 |
|
---|
| 1515 | enddo
|
---|
| 1516 | \end_layout
|
---|
| 1517 |
|
---|
| 1518 | \begin_layout Standard
|
---|
| 1519 |
|
---|
| 1520 |
|
---|
| 1521 | \backslash
|
---|
| 1522 | end{lstlisting}
|
---|
| 1523 | \end_layout
|
---|
| 1524 |
|
---|
| 1525 | \end_inset
|
---|
| 1526 |
|
---|
| 1527 |
|
---|
| 1528 | \begin_inset Float table
|
---|
| 1529 | placement p
|
---|
| 1530 | wide false
|
---|
| 1531 | sideways false
|
---|
| 1532 | status collapsed
|
---|
| 1533 |
|
---|
| 1534 | \begin_layout Standard
|
---|
| 1535 | \begin_inset Tabular
|
---|
| 1536 | <lyxtabular version="3" rows="9" columns="3">
|
---|
| 1537 | <features>
|
---|
| 1538 | <column alignment="center" valignment="top" leftline="true" width="0">
|
---|
| 1539 | <column alignment="center" valignment="top" leftline="true" width="0">
|
---|
| 1540 | <column alignment="left" valignment="top" leftline="true" rightline="true" width="35col%">
|
---|
| 1541 | <row topline="true" bottomline="true">
|
---|
| 1542 | <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
|
---|
| 1543 | \begin_inset Text
|
---|
| 1544 |
|
---|
| 1545 | \begin_layout Standard
|
---|
| 1546 | Variable Name
|
---|
| 1547 | \end_layout
|
---|
| 1548 |
|
---|
| 1549 | \end_inset
|
---|
| 1550 | </cell>
|
---|
| 1551 | <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
|
---|
| 1552 | \begin_inset Text
|
---|
| 1553 |
|
---|
| 1554 | \begin_layout Standard
|
---|
| 1555 | Type
|
---|
| 1556 | \end_layout
|
---|
| 1557 |
|
---|
| 1558 | \end_inset
|
---|
| 1559 | </cell>
|
---|
| 1560 | <cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
|
---|
| 1561 | \begin_inset Text
|
---|
| 1562 |
|
---|
| 1563 | \begin_layout Standard
|
---|
| 1564 | Description
|
---|
| 1565 | \end_layout
|
---|
| 1566 |
|
---|
| 1567 | \end_inset
|
---|
| 1568 | </cell>
|
---|
| 1569 | </row>
|
---|
| 1570 | <row topline="true">
|
---|
| 1571 | <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
|
---|
| 1572 | \begin_inset Text
|
---|
| 1573 |
|
---|
| 1574 | \begin_layout Standard
|
---|
| 1575 | ityat
|
---|
| 1576 | \end_layout
|
---|
| 1577 |
|
---|
| 1578 | \end_inset
|
---|
| 1579 | </cell>
|
---|
| 1580 | <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
|
---|
| 1581 | \begin_inset Text
|
---|
| 1582 |
|
---|
| 1583 | \begin_layout Standard
|
---|
| 1584 | array of int
|
---|
| 1585 | \end_layout
|
---|
| 1586 |
|
---|
| 1587 | \end_inset
|
---|
| 1588 | </cell>
|
---|
| 1589 | <cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
|
---|
| 1590 | \begin_inset Text
|
---|
| 1591 |
|
---|
| 1592 | \begin_layout Standard
|
---|
| 1593 | Index of type of atom
|
---|
| 1594 | \end_layout
|
---|
| 1595 |
|
---|
| 1596 | \end_inset
|
---|
| 1597 | </cell>
|
---|
| 1598 | </row>
|
---|
| 1599 | <row topline="true">
|
---|
| 1600 | <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
|
---|
| 1601 | \begin_inset Text
|
---|
| 1602 |
|
---|
| 1603 | \begin_layout Standard
|
---|
| 1604 | xat, yat, zat
|
---|
| 1605 | \end_layout
|
---|
| 1606 |
|
---|
| 1607 | \end_inset
|
---|
| 1608 | </cell>
|
---|
| 1609 | <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
|
---|
| 1610 | \begin_inset Text
|
---|
| 1611 |
|
---|
| 1612 | \begin_layout Standard
|
---|
| 1613 | arrays of double
|
---|
| 1614 | \end_layout
|
---|
| 1615 |
|
---|
| 1616 | \end_inset
|
---|
| 1617 | </cell>
|
---|
| 1618 | <cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
|
---|
| 1619 | \begin_inset Text
|
---|
| 1620 |
|
---|
| 1621 | \begin_layout Standard
|
---|
| 1622 | Cartesian coordinates of atom
|
---|
| 1623 | \end_layout
|
---|
| 1624 |
|
---|
| 1625 | \end_inset
|
---|
| 1626 | </cell>
|
---|
| 1627 | </row>
|
---|
| 1628 | <row topline="true">
|
---|
| 1629 | <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
|
---|
| 1630 | \begin_inset Text
|
---|
| 1631 |
|
---|
| 1632 | \begin_layout Standard
|
---|
| 1633 | cgat
|
---|
| 1634 | \end_layout
|
---|
| 1635 |
|
---|
| 1636 | \end_inset
|
---|
| 1637 | </cell>
|
---|
| 1638 | <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
|
---|
| 1639 | \begin_inset Text
|
---|
| 1640 |
|
---|
| 1641 | \begin_layout Standard
|
---|
| 1642 | array of double
|
---|
| 1643 | \end_layout
|
---|
| 1644 |
|
---|
| 1645 | \end_inset
|
---|
| 1646 | </cell>
|
---|
| 1647 | <cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
|
---|
| 1648 | \begin_inset Text
|
---|
| 1649 |
|
---|
| 1650 | \begin_layout Standard
|
---|
| 1651 | Partial electric charge on atom
|
---|
| 1652 | \end_layout
|
---|
| 1653 |
|
---|
| 1654 | \end_inset
|
---|
| 1655 | </cell>
|
---|
| 1656 | </row>
|
---|
| 1657 | <row topline="true">
|
---|
| 1658 | <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
|
---|
| 1659 | \begin_inset Text
|
---|
| 1660 |
|
---|
| 1661 | \begin_layout Standard
|
---|
| 1662 | nmat
|
---|
| 1663 | \end_layout
|
---|
| 1664 |
|
---|
| 1665 | \end_inset
|
---|
| 1666 | </cell>
|
---|
| 1667 | <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
|
---|
| 1668 | \begin_inset Text
|
---|
| 1669 |
|
---|
| 1670 | \begin_layout Standard
|
---|
| 1671 | array of character*4
|
---|
| 1672 | \end_layout
|
---|
| 1673 |
|
---|
| 1674 | \end_inset
|
---|
| 1675 | </cell>
|
---|
| 1676 | <cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
|
---|
| 1677 | \begin_inset Text
|
---|
| 1678 |
|
---|
| 1679 | \begin_layout Standard
|
---|
| 1680 | Name of atom, e.g., C, N, O, H1, H2
|
---|
| 1681 | \end_layout
|
---|
| 1682 |
|
---|
| 1683 | \end_inset
|
---|
| 1684 | </cell>
|
---|
| 1685 | </row>
|
---|
| 1686 | <row topline="true">
|
---|
| 1687 | <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
|
---|
| 1688 | \begin_inset Text
|
---|
| 1689 |
|
---|
| 1690 | \begin_layout Standard
|
---|
| 1691 | iowat
|
---|
| 1692 | \end_layout
|
---|
| 1693 |
|
---|
| 1694 | \end_inset
|
---|
| 1695 | </cell>
|
---|
| 1696 | <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
|
---|
| 1697 | \begin_inset Text
|
---|
| 1698 |
|
---|
| 1699 | \begin_layout Standard
|
---|
| 1700 | array of int
|
---|
| 1701 | \end_layout
|
---|
| 1702 |
|
---|
| 1703 | \end_inset
|
---|
| 1704 | </cell>
|
---|
| 1705 | <cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
|
---|
| 1706 | \begin_inset Text
|
---|
| 1707 |
|
---|
| 1708 | \begin_layout Standard
|
---|
| 1709 | Index of preceeding atom (see Fig.\InsetSpace ~
|
---|
| 1710 |
|
---|
| 1711 | \begin_inset LatexCommand ref
|
---|
| 1712 | reference "fig:Enumeration-of-atoms"
|
---|
| 1713 |
|
---|
| 1714 | \end_inset
|
---|
| 1715 |
|
---|
| 1716 | ), 0 if no preceeding atom.
|
---|
| 1717 | \end_layout
|
---|
| 1718 |
|
---|
| 1719 | \end_inset
|
---|
| 1720 | </cell>
|
---|
| 1721 | </row>
|
---|
| 1722 | <row topline="true">
|
---|
| 1723 | <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
|
---|
| 1724 | \begin_inset Text
|
---|
| 1725 |
|
---|
| 1726 | \begin_layout Standard
|
---|
| 1727 | iyowat
|
---|
| 1728 | \end_layout
|
---|
| 1729 |
|
---|
| 1730 | \end_inset
|
---|
| 1731 | </cell>
|
---|
| 1732 | <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
|
---|
| 1733 | \begin_inset Text
|
---|
| 1734 |
|
---|
| 1735 | \begin_layout Standard
|
---|
| 1736 | array of int
|
---|
| 1737 | \end_layout
|
---|
| 1738 |
|
---|
| 1739 | \end_inset
|
---|
| 1740 | </cell>
|
---|
| 1741 | <cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
|
---|
| 1742 | \begin_inset Text
|
---|
| 1743 |
|
---|
| 1744 | \begin_layout Standard
|
---|
| 1745 | Type of bond with preceeding atom.
|
---|
| 1746 | \begin_inset Note Note
|
---|
| 1747 | status open
|
---|
| 1748 |
|
---|
| 1749 | \begin_layout Standard
|
---|
| 1750 | Maybe, this should be called ityinbdat.
|
---|
| 1751 | \end_layout
|
---|
| 1752 |
|
---|
| 1753 | \end_inset
|
---|
| 1754 |
|
---|
| 1755 |
|
---|
| 1756 | \end_layout
|
---|
| 1757 |
|
---|
| 1758 | \end_inset
|
---|
| 1759 | </cell>
|
---|
| 1760 | </row>
|
---|
| 1761 | <row topline="true" bottomline="true">
|
---|
| 1762 | <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
|
---|
| 1763 | \begin_inset Text
|
---|
| 1764 |
|
---|
| 1765 | \begin_layout Standard
|
---|
| 1766 | nbdat
|
---|
| 1767 | \end_layout
|
---|
| 1768 |
|
---|
| 1769 | \end_inset
|
---|
| 1770 | </cell>
|
---|
| 1771 | <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
|
---|
| 1772 | \begin_inset Text
|
---|
| 1773 |
|
---|
| 1774 | \begin_layout Standard
|
---|
| 1775 | array of int
|
---|
| 1776 | \end_layout
|
---|
| 1777 |
|
---|
| 1778 | \end_inset
|
---|
| 1779 | </cell>
|
---|
| 1780 | <cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
|
---|
| 1781 | \begin_inset Text
|
---|
| 1782 |
|
---|
| 1783 | \begin_layout Standard
|
---|
| 1784 | Number of bonds to succeeding atom (outgoing bonds)
|
---|
| 1785 | \end_layout
|
---|
| 1786 |
|
---|
| 1787 | \end_inset
|
---|
| 1788 | </cell>
|
---|
| 1789 | </row>
|
---|
| 1790 | <row bottomline="true">
|
---|
| 1791 | <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
|
---|
| 1792 | \begin_inset Text
|
---|
| 1793 |
|
---|
| 1794 | \begin_layout Standard
|
---|
| 1795 | ibdat
|
---|
| 1796 | \end_layout
|
---|
| 1797 |
|
---|
| 1798 | \end_inset
|
---|
| 1799 | </cell>
|
---|
| 1800 | <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
|
---|
| 1801 | \begin_inset Text
|
---|
| 1802 |
|
---|
| 1803 | \begin_layout Standard
|
---|
| 1804 | two dimensional array of int
|
---|
| 1805 | \end_layout
|
---|
| 1806 |
|
---|
| 1807 | \end_inset
|
---|
| 1808 | </cell>
|
---|
| 1809 | <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
|
---|
| 1810 | \begin_inset Text
|
---|
| 1811 |
|
---|
| 1812 | \begin_layout Standard
|
---|
| 1813 | Indices of successor atoms
|
---|
| 1814 | \end_layout
|
---|
| 1815 |
|
---|
| 1816 | \end_inset
|
---|
| 1817 | </cell>
|
---|
| 1818 | </row>
|
---|
| 1819 | </lyxtabular>
|
---|
| 1820 |
|
---|
| 1821 | \end_inset
|
---|
| 1822 |
|
---|
| 1823 |
|
---|
| 1824 | \end_layout
|
---|
| 1825 |
|
---|
| 1826 | \begin_layout Standard
|
---|
| 1827 | \begin_inset Caption
|
---|
| 1828 |
|
---|
| 1829 | \begin_layout Standard
|
---|
| 1830 | \begin_inset LatexCommand label
|
---|
| 1831 | name "tab:atomic-properties"
|
---|
| 1832 |
|
---|
| 1833 | \end_inset
|
---|
| 1834 |
|
---|
| 1835 | List of variables storing atomic properties.
|
---|
| 1836 | All the properties of atom
|
---|
| 1837 | \begin_inset Formula $i$
|
---|
| 1838 | \end_inset
|
---|
| 1839 |
|
---|
| 1840 | are accessed as the
|
---|
| 1841 | \begin_inset Formula $i$
|
---|
| 1842 | \end_inset
|
---|
| 1843 |
|
---|
| 1844 | th element of the arrays.
|
---|
| 1845 | \end_layout
|
---|
| 1846 |
|
---|
| 1847 | \end_inset
|
---|
| 1848 |
|
---|
| 1849 |
|
---|
| 1850 | \end_layout
|
---|
| 1851 |
|
---|
| 1852 | \end_inset
|
---|
| 1853 |
|
---|
| 1854 |
|
---|
| 1855 | \begin_inset Float table
|
---|
| 1856 | placement p
|
---|
| 1857 | wide false
|
---|
| 1858 | sideways false
|
---|
| 1859 | status collapsed
|
---|
| 1860 |
|
---|
| 1861 | \begin_layout Standard
|
---|
| 1862 | \begin_inset Tabular
|
---|
| 1863 | <lyxtabular version="3" rows="8" columns="3">
|
---|
| 1864 | <features>
|
---|
| 1865 | <column alignment="center" valignment="top" leftline="true" width="0">
|
---|
| 1866 | <column alignment="center" valignment="top" leftline="true" width="0">
|
---|
| 1867 | <column alignment="center" valignment="top" leftline="true" rightline="true" width="35col%">
|
---|
| 1868 | <row topline="true" bottomline="true">
|
---|
| 1869 | <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
|
---|
| 1870 | \begin_inset Text
|
---|
| 1871 |
|
---|
| 1872 | \begin_layout Standard
|
---|
| 1873 | Name
|
---|
| 1874 | \end_layout
|
---|
| 1875 |
|
---|
| 1876 | \end_inset
|
---|
| 1877 | </cell>
|
---|
| 1878 | <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
|
---|
| 1879 | \begin_inset Text
|
---|
| 1880 |
|
---|
| 1881 | \begin_layout Standard
|
---|
| 1882 | Type
|
---|
| 1883 | \end_layout
|
---|
| 1884 |
|
---|
| 1885 | \end_inset
|
---|
| 1886 | </cell>
|
---|
| 1887 | <cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
|
---|
| 1888 | \begin_inset Text
|
---|
| 1889 |
|
---|
| 1890 | \begin_layout Standard
|
---|
| 1891 | Description
|
---|
| 1892 | \end_layout
|
---|
| 1893 |
|
---|
| 1894 | \end_inset
|
---|
| 1895 | </cell>
|
---|
| 1896 | </row>
|
---|
| 1897 | <row topline="true">
|
---|
| 1898 | <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
|
---|
| 1899 | \begin_inset Text
|
---|
| 1900 |
|
---|
| 1901 | \begin_layout Standard
|
---|
| 1902 | xbaat, ybaat, zbaat
|
---|
| 1903 | \end_layout
|
---|
| 1904 |
|
---|
| 1905 | \end_inset
|
---|
| 1906 | </cell>
|
---|
| 1907 | <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
|
---|
| 1908 | \begin_inset Text
|
---|
| 1909 |
|
---|
| 1910 | \begin_layout Standard
|
---|
| 1911 | 3 arrays of double
|
---|
| 1912 | \end_layout
|
---|
| 1913 |
|
---|
| 1914 | \end_inset
|
---|
| 1915 | </cell>
|
---|
| 1916 | <cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
|
---|
| 1917 | \begin_inset Text
|
---|
| 1918 |
|
---|
| 1919 | \begin_layout Standard
|
---|
| 1920 | Rotation axis for valence angle.
|
---|
| 1921 | (see Fig.
|
---|
| 1922 | )
|
---|
| 1923 | \end_layout
|
---|
| 1924 |
|
---|
| 1925 | \end_inset
|
---|
| 1926 | </cell>
|
---|
| 1927 | </row>
|
---|
| 1928 | <row topline="true">
|
---|
| 1929 | <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
|
---|
| 1930 | \begin_inset Text
|
---|
| 1931 |
|
---|
| 1932 | \begin_layout Standard
|
---|
| 1933 | baat
|
---|
| 1934 | \end_layout
|
---|
| 1935 |
|
---|
| 1936 | \end_inset
|
---|
| 1937 | </cell>
|
---|
| 1938 | <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
|
---|
| 1939 | \begin_inset Text
|
---|
| 1940 |
|
---|
| 1941 | \begin_layout Standard
|
---|
| 1942 | array of double
|
---|
| 1943 | \end_layout
|
---|
| 1944 |
|
---|
| 1945 | \end_inset
|
---|
| 1946 | </cell>
|
---|
| 1947 | <cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
|
---|
| 1948 | \begin_inset Text
|
---|
| 1949 |
|
---|
| 1950 | \begin_layout Standard
|
---|
| 1951 | Valence angle in radians
|
---|
| 1952 | \end_layout
|
---|
| 1953 |
|
---|
| 1954 | \end_inset
|
---|
| 1955 | </cell>
|
---|
| 1956 | </row>
|
---|
| 1957 | <row topline="true">
|
---|
| 1958 | <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
|
---|
| 1959 | \begin_inset Text
|
---|
| 1960 |
|
---|
| 1961 | \begin_layout Standard
|
---|
| 1962 | xtoat, ytoat, ztoat
|
---|
| 1963 | \end_layout
|
---|
| 1964 |
|
---|
| 1965 | \end_inset
|
---|
| 1966 | </cell>
|
---|
| 1967 | <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
|
---|
| 1968 | \begin_inset Text
|
---|
| 1969 |
|
---|
| 1970 | \begin_layout Standard
|
---|
| 1971 | 3 arrays of double
|
---|
| 1972 | \end_layout
|
---|
| 1973 |
|
---|
| 1974 | \end_inset
|
---|
| 1975 | </cell>
|
---|
| 1976 | <cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
|
---|
| 1977 | \begin_inset Text
|
---|
| 1978 |
|
---|
| 1979 | \begin_layout Standard
|
---|
| 1980 | Rotation axis for dihedral (torsion) angle.
|
---|
| 1981 | (see Fig.)
|
---|
| 1982 | \end_layout
|
---|
| 1983 |
|
---|
| 1984 | \end_inset
|
---|
| 1985 | </cell>
|
---|
| 1986 | </row>
|
---|
| 1987 | <row topline="true">
|
---|
| 1988 | <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
|
---|
| 1989 | \begin_inset Text
|
---|
| 1990 |
|
---|
| 1991 | \begin_layout Standard
|
---|
| 1992 | toat
|
---|
| 1993 | \end_layout
|
---|
| 1994 |
|
---|
| 1995 | \end_inset
|
---|
| 1996 | </cell>
|
---|
| 1997 | <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
|
---|
| 1998 | \begin_inset Text
|
---|
| 1999 |
|
---|
| 2000 | \begin_layout Standard
|
---|
| 2001 | array of double
|
---|
| 2002 | \end_layout
|
---|
| 2003 |
|
---|
| 2004 | \end_inset
|
---|
| 2005 | </cell>
|
---|
| 2006 | <cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
|
---|
| 2007 | \begin_inset Text
|
---|
| 2008 |
|
---|
| 2009 | \begin_layout Standard
|
---|
| 2010 | Torsion angle defined by iowat(iowat(iowat(i))), iowat(iowat(i)), iowat(i),
|
---|
| 2011 | i in radians (see Fig.)
|
---|
| 2012 | \end_layout
|
---|
| 2013 |
|
---|
| 2014 | \end_inset
|
---|
| 2015 | </cell>
|
---|
| 2016 | </row>
|
---|
| 2017 | <row topline="true">
|
---|
| 2018 | <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
|
---|
| 2019 | \begin_inset Text
|
---|
| 2020 |
|
---|
| 2021 | \begin_layout Standard
|
---|
| 2022 | blat
|
---|
| 2023 | \end_layout
|
---|
| 2024 |
|
---|
| 2025 | \end_inset
|
---|
| 2026 | </cell>
|
---|
| 2027 | <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
|
---|
| 2028 | \begin_inset Text
|
---|
| 2029 |
|
---|
| 2030 | \begin_layout Standard
|
---|
| 2031 | array of double
|
---|
| 2032 | \end_layout
|
---|
| 2033 |
|
---|
| 2034 | \end_inset
|
---|
| 2035 | </cell>
|
---|
| 2036 | <cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
|
---|
| 2037 | \begin_inset Text
|
---|
| 2038 |
|
---|
| 2039 | \begin_layout Standard
|
---|
| 2040 | Length of bond.
|
---|
| 2041 | \end_layout
|
---|
| 2042 |
|
---|
| 2043 | \end_inset
|
---|
| 2044 | </cell>
|
---|
| 2045 | </row>
|
---|
| 2046 | <row topline="true">
|
---|
| 2047 | <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
|
---|
| 2048 | \begin_inset Text
|
---|
| 2049 |
|
---|
| 2050 | \begin_layout Standard
|
---|
| 2051 | ixmsat
|
---|
| 2052 | \end_layout
|
---|
| 2053 |
|
---|
| 2054 | \end_inset
|
---|
| 2055 | </cell>
|
---|
| 2056 | <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
|
---|
| 2057 | \begin_inset Text
|
---|
| 2058 |
|
---|
| 2059 | \begin_layout Standard
|
---|
| 2060 | array of int
|
---|
| 2061 | \end_layout
|
---|
| 2062 |
|
---|
| 2063 | \end_inset
|
---|
| 2064 | </cell>
|
---|
| 2065 | <cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
|
---|
| 2066 | \begin_inset Text
|
---|
| 2067 |
|
---|
| 2068 | \begin_layout Standard
|
---|
| 2069 | Index of moving set belonging to atom
|
---|
| 2070 | \end_layout
|
---|
| 2071 |
|
---|
| 2072 | \end_inset
|
---|
| 2073 | </cell>
|
---|
| 2074 | </row>
|
---|
| 2075 | <row topline="true" bottomline="true">
|
---|
| 2076 | <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
|
---|
| 2077 | \begin_inset Text
|
---|
| 2078 |
|
---|
| 2079 | \begin_layout Standard
|
---|
| 2080 |
|
---|
| 2081 | \end_layout
|
---|
| 2082 |
|
---|
| 2083 | \end_inset
|
---|
| 2084 | </cell>
|
---|
| 2085 | <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
|
---|
| 2086 | \begin_inset Text
|
---|
| 2087 |
|
---|
| 2088 | \begin_layout Standard
|
---|
| 2089 |
|
---|
| 2090 | \end_layout
|
---|
| 2091 |
|
---|
| 2092 | \end_inset
|
---|
| 2093 | </cell>
|
---|
| 2094 | <cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
|
---|
| 2095 | \begin_inset Text
|
---|
| 2096 |
|
---|
| 2097 | \begin_layout Standard
|
---|
| 2098 |
|
---|
| 2099 | \end_layout
|
---|
| 2100 |
|
---|
| 2101 | \end_inset
|
---|
| 2102 | </cell>
|
---|
| 2103 | </row>
|
---|
| 2104 | </lyxtabular>
|
---|
| 2105 |
|
---|
| 2106 | \end_inset
|
---|
| 2107 |
|
---|
| 2108 |
|
---|
| 2109 | \end_layout
|
---|
| 2110 |
|
---|
| 2111 | \begin_layout Standard
|
---|
| 2112 | \begin_inset Caption
|
---|
| 2113 |
|
---|
| 2114 | \begin_layout Standard
|
---|
| 2115 | \begin_inset LatexCommand label
|
---|
| 2116 | name "tab:dihedral-to-atom"
|
---|
| 2117 |
|
---|
| 2118 | \end_inset
|
---|
| 2119 |
|
---|
| 2120 | Each dihedral and valence angle and the corresponding moving set is associated
|
---|
| 2121 | with a covalent bond which in turn is defined by its tail atom.
|
---|
| 2122 | This table list the related variables.
|
---|
| 2123 |
|
---|
| 2124 | \end_layout
|
---|
| 2125 |
|
---|
| 2126 | \end_inset
|
---|
| 2127 |
|
---|
| 2128 |
|
---|
| 2129 | \end_layout
|
---|
| 2130 |
|
---|
| 2131 | \end_inset
|
---|
| 2132 |
|
---|
| 2133 |
|
---|
| 2134 | \begin_inset Float figure
|
---|
| 2135 | wide false
|
---|
| 2136 | sideways false
|
---|
| 2137 | status collapsed
|
---|
| 2138 |
|
---|
| 2139 | \begin_layout Standard
|
---|
| 2140 | \align center
|
---|
| 2141 | \begin_inset Graphics
|
---|
| 2142 | filename angle_defs.eps
|
---|
| 2143 | scaleBeforeRotation
|
---|
| 2144 | subcaption
|
---|
| 2145 |
|
---|
| 2146 | \end_inset
|
---|
| 2147 |
|
---|
| 2148 |
|
---|
| 2149 | \begin_inset Graphics
|
---|
| 2150 | filename dihedral_defs.eps
|
---|
| 2151 | scaleBeforeRotation
|
---|
| 2152 | subcaption
|
---|
| 2153 |
|
---|
| 2154 | \end_inset
|
---|
| 2155 |
|
---|
| 2156 |
|
---|
| 2157 | \end_layout
|
---|
| 2158 |
|
---|
| 2159 | \begin_layout Standard
|
---|
| 2160 | \begin_inset Caption
|
---|
| 2161 |
|
---|
| 2162 | \begin_layout Standard
|
---|
| 2163 | \begin_inset LatexCommand label
|
---|
| 2164 | name "fig:angle-defs-in-SMMP"
|
---|
| 2165 |
|
---|
| 2166 | \end_inset
|
---|
| 2167 |
|
---|
| 2168 | Angle in SMMP.
|
---|
| 2169 | There are two different types of angles in SMMP (and proteins in general):
|
---|
| 2170 | bond and torsional angles.
|
---|
| 2171 | The bond or valence angle is show in (a).
|
---|
| 2172 | The red arrow indicates the rotation axis and is proportional to the cross
|
---|
| 2173 | product of the two bonds
|
---|
| 2174 | \begin_inset Formula $(1,4)$
|
---|
| 2175 | \end_inset
|
---|
| 2176 |
|
---|
| 2177 | and
|
---|
| 2178 | \begin_inset Formula $(4,25)$
|
---|
| 2179 | \end_inset
|
---|
| 2180 |
|
---|
| 2181 | making up the angle.
|
---|
| 2182 | The angle
|
---|
| 2183 | \begin_inset Formula $\alpha$
|
---|
| 2184 | \end_inset
|
---|
| 2185 |
|
---|
| 2186 | is associated with atom
|
---|
| 2187 | \begin_inset Formula $4$
|
---|
| 2188 | \end_inset
|
---|
| 2189 |
|
---|
| 2190 | .
|
---|
| 2191 | The dihedral or torsional angles are rotations around a bond and determined
|
---|
| 2192 | by the angles between the two adjacent planes.
|
---|
| 2193 | For example, the angle
|
---|
| 2194 | \begin_inset Formula $\psi$
|
---|
| 2195 | \end_inset
|
---|
| 2196 |
|
---|
| 2197 | in (b) is the angle between the plane defined by atoms 1, 4, and 25, and
|
---|
| 2198 | the plane defined by 4, 25, and 28.
|
---|
| 2199 | We could therefore reference this angle using the quadruplet (1, 4, 25,
|
---|
| 2200 | 28).
|
---|
| 2201 | Note that atom 1 is the predecessor of atom 4, atom 4 the predecessor of
|
---|
| 2202 | 25, and, finally, atom 25 the predecessor of 28.
|
---|
| 2203 | SMMP uses this relation to associate the angle
|
---|
| 2204 | \begin_inset Formula $\psi$
|
---|
| 2205 | \end_inset
|
---|
| 2206 |
|
---|
| 2207 | with atom 28.
|
---|
| 2208 | \end_layout
|
---|
| 2209 |
|
---|
| 2210 | \end_inset
|
---|
| 2211 |
|
---|
| 2212 |
|
---|
| 2213 | \end_layout
|
---|
| 2214 |
|
---|
| 2215 | \end_inset
|
---|
| 2216 |
|
---|
| 2217 |
|
---|
| 2218 | \end_layout
|
---|
| 2219 |
|
---|
| 2220 | \begin_layout Standard
|
---|
| 2221 | Table
|
---|
| 2222 | \begin_inset LatexCommand ref
|
---|
| 2223 | reference "tab:atomic-properties"
|
---|
| 2224 |
|
---|
| 2225 | \end_inset
|
---|
| 2226 |
|
---|
| 2227 | lists the arrays containing the atomic properties such as charge, position,
|
---|
| 2228 | and in- and outgoing bonds.
|
---|
| 2229 | In the standard geometry configurations can defined by the dihedral angles.
|
---|
| 2230 | The variables associated with the angles are given in Table
|
---|
| 2231 | \begin_inset LatexCommand ref
|
---|
| 2232 | reference "tab:dihedral-to-atom"
|
---|
| 2233 |
|
---|
| 2234 | \end_inset
|
---|
| 2235 |
|
---|
| 2236 | and a description of the angles can be found in Fig.\InsetSpace ~
|
---|
| 2237 |
|
---|
| 2238 | \begin_inset LatexCommand ref
|
---|
| 2239 | reference "fig:angle-defs-in-SMMP"
|
---|
| 2240 |
|
---|
| 2241 | \end_inset
|
---|
| 2242 |
|
---|
| 2243 | .
|
---|
| 2244 | \end_layout
|
---|
| 2245 |
|
---|
| 2246 | \begin_layout Paragraph
|
---|
| 2247 | \begin_inset Note Note
|
---|
| 2248 | status open
|
---|
| 2249 |
|
---|
| 2250 | \begin_layout Standard
|
---|
| 2251 | Why are the names so short and what do they mean?
|
---|
| 2252 | \end_layout
|
---|
| 2253 |
|
---|
| 2254 | \begin_layout Paragraph
|
---|
| 2255 | Setting up a force field
|
---|
| 2256 | \end_layout
|
---|
| 2257 |
|
---|
| 2258 | \begin_layout Paragraph
|
---|
| 2259 | Loading a molecule from a .seq and .var file
|
---|
| 2260 | \end_layout
|
---|
| 2261 |
|
---|
| 2262 | \begin_layout Standard
|
---|
| 2263 | fixed variables, default values, access?
|
---|
| 2264 | \end_layout
|
---|
| 2265 |
|
---|
| 2266 | \begin_layout Paragraph
|
---|
| 2267 | Loading a molecule from a PDB file
|
---|
| 2268 | \end_layout
|
---|
| 2269 |
|
---|
| 2270 | \begin_layout Standard
|
---|
| 2271 | where are things stored? what does regularization do?
|
---|
| 2272 | \end_layout
|
---|
| 2273 |
|
---|
| 2274 | \end_inset
|
---|
| 2275 |
|
---|
| 2276 |
|
---|
| 2277 | \end_layout
|
---|
| 2278 |
|
---|
| 2279 | \begin_layout Section
|
---|
| 2280 | Limitations
|
---|
| 2281 | \end_layout
|
---|
| 2282 |
|
---|
| 2283 | \begin_layout Standard
|
---|
| 2284 | All parameters which limit the usage of SMMP are stored in the file INCL.H.
|
---|
| 2285 | The most important ones are listed below.
|
---|
| 2286 | The values of these parameters should be changed only in a consistent way!
|
---|
| 2287 |
|
---|
| 2288 | \begin_inset ERT
|
---|
| 2289 | status collapsed
|
---|
| 2290 |
|
---|
| 2291 | \begin_layout Standard
|
---|
| 2292 |
|
---|
| 2293 |
|
---|
| 2294 | \backslash
|
---|
| 2295 | begin{verbatim}
|
---|
| 2296 | \end_layout
|
---|
| 2297 |
|
---|
| 2298 | \begin_layout Standard
|
---|
| 2299 |
|
---|
| 2300 | \end_layout
|
---|
| 2301 |
|
---|
| 2302 | \begin_layout Standard
|
---|
| 2303 |
|
---|
| 2304 | mxml=1 max.
|
---|
| 2305 | number of molecules
|
---|
| 2306 | \end_layout
|
---|
| 2307 |
|
---|
| 2308 | \begin_layout Standard
|
---|
| 2309 |
|
---|
| 2310 | \end_layout
|
---|
| 2311 |
|
---|
| 2312 | \begin_layout Standard
|
---|
| 2313 |
|
---|
| 2314 | mxrs=100 max.
|
---|
| 2315 | total number of residues
|
---|
| 2316 | \end_layout
|
---|
| 2317 |
|
---|
| 2318 | \begin_layout Standard
|
---|
| 2319 |
|
---|
| 2320 | \end_layout
|
---|
| 2321 |
|
---|
| 2322 | \begin_layout Standard
|
---|
| 2323 |
|
---|
| 2324 | mxat=2000 max.
|
---|
| 2325 | total number of atoms
|
---|
| 2326 | \end_layout
|
---|
| 2327 |
|
---|
| 2328 | \begin_layout Standard
|
---|
| 2329 |
|
---|
| 2330 | \end_layout
|
---|
| 2331 |
|
---|
| 2332 | \begin_layout Standard
|
---|
| 2333 |
|
---|
| 2334 | mxbd=3 max.
|
---|
| 2335 | number of bonds to following atoms
|
---|
| 2336 | \end_layout
|
---|
| 2337 |
|
---|
| 2338 | \begin_layout Standard
|
---|
| 2339 |
|
---|
| 2340 | \end_layout
|
---|
| 2341 |
|
---|
| 2342 | \begin_layout Standard
|
---|
| 2343 |
|
---|
| 2344 | mxvr=mxrs*5 max.
|
---|
| 2345 | number of local variables
|
---|
| 2346 | \end_layout
|
---|
| 2347 |
|
---|
| 2348 | \begin_layout Standard
|
---|
| 2349 |
|
---|
| 2350 | \end_layout
|
---|
| 2351 |
|
---|
| 2352 | \begin_layout Standard
|
---|
| 2353 |
|
---|
| 2354 | mxms=mxvr*3 max.
|
---|
| 2355 | total number of moving sets
|
---|
| 2356 | \end_layout
|
---|
| 2357 |
|
---|
| 2358 | \begin_layout Standard
|
---|
| 2359 |
|
---|
| 2360 | \end_layout
|
---|
| 2361 |
|
---|
| 2362 | \begin_layout Standard
|
---|
| 2363 |
|
---|
| 2364 | mxvw=mxat*4 max.
|
---|
| 2365 | number of vdw domains
|
---|
| 2366 | \end_layout
|
---|
| 2367 |
|
---|
| 2368 | \begin_layout Standard
|
---|
| 2369 |
|
---|
| 2370 | \end_layout
|
---|
| 2371 |
|
---|
| 2372 | \begin_layout Standard
|
---|
| 2373 |
|
---|
| 2374 | mx14=mxat*4 max.
|
---|
| 2375 | number of '1-4' partners
|
---|
| 2376 | \end_layout
|
---|
| 2377 |
|
---|
| 2378 | \begin_layout Standard
|
---|
| 2379 |
|
---|
| 2380 | \end_layout
|
---|
| 2381 |
|
---|
| 2382 | \begin_layout Standard
|
---|
| 2383 |
|
---|
| 2384 | mxath=100, max.
|
---|
| 2385 | number of atoms in help-arrays
|
---|
| 2386 | \end_layout
|
---|
| 2387 |
|
---|
| 2388 | \begin_layout Standard
|
---|
| 2389 |
|
---|
| 2390 | \end_layout
|
---|
| 2391 |
|
---|
| 2392 | \begin_layout Standard
|
---|
| 2393 |
|
---|
| 2394 | mxvrh=mxath max.
|
---|
| 2395 | number of variables in help
|
---|
| 2396 | \end_layout
|
---|
| 2397 |
|
---|
| 2398 | \begin_layout Standard
|
---|
| 2399 |
|
---|
| 2400 | \end_layout
|
---|
| 2401 |
|
---|
| 2402 | \begin_layout Standard
|
---|
| 2403 |
|
---|
| 2404 | mxtyat=18 max.
|
---|
| 2405 | number of energetic atom-types
|
---|
| 2406 | \end_layout
|
---|
| 2407 |
|
---|
| 2408 | \begin_layout Standard
|
---|
| 2409 |
|
---|
| 2410 | \end_layout
|
---|
| 2411 |
|
---|
| 2412 | \begin_layout Standard
|
---|
| 2413 |
|
---|
| 2414 | mxhbdo=4 max.
|
---|
| 2415 | types of Hydrogens as donors in HB
|
---|
| 2416 | \end_layout
|
---|
| 2417 |
|
---|
| 2418 | \begin_layout Standard
|
---|
| 2419 |
|
---|
| 2420 | \end_layout
|
---|
| 2421 |
|
---|
| 2422 | \begin_layout Standard
|
---|
| 2423 |
|
---|
| 2424 | mxhbac=6 max.
|
---|
| 2425 | types of atoms as acceptors in HB
|
---|
| 2426 | \end_layout
|
---|
| 2427 |
|
---|
| 2428 | \begin_layout Standard
|
---|
| 2429 |
|
---|
| 2430 | \end_layout
|
---|
| 2431 |
|
---|
| 2432 | \begin_layout Standard
|
---|
| 2433 |
|
---|
| 2434 | mxtyto=19 max.
|
---|
| 2435 | number of types of torsional potentials
|
---|
| 2436 | \end_layout
|
---|
| 2437 |
|
---|
| 2438 | \begin_layout Standard
|
---|
| 2439 |
|
---|
| 2440 | \end_layout
|
---|
| 2441 |
|
---|
| 2442 | \begin_layout Standard
|
---|
| 2443 |
|
---|
| 2444 | nrsty=35 max.
|
---|
| 2445 | number of residue types
|
---|
| 2446 | \end_layout
|
---|
| 2447 |
|
---|
| 2448 | \begin_layout Standard
|
---|
| 2449 |
|
---|
| 2450 | \end_layout
|
---|
| 2451 |
|
---|
| 2452 | \begin_layout Standard
|
---|
| 2453 |
|
---|
| 2454 | mxtysol=9 the number of solvation parameters sets
|
---|
| 2455 | \end_layout
|
---|
| 2456 |
|
---|
| 2457 | \begin_layout Standard
|
---|
| 2458 |
|
---|
| 2459 | \end_layout
|
---|
| 2460 |
|
---|
| 2461 | \begin_layout Standard
|
---|
| 2462 |
|
---|
| 2463 |
|
---|
| 2464 | \backslash
|
---|
| 2465 | end{verbatim}
|
---|
| 2466 | \end_layout
|
---|
| 2467 |
|
---|
| 2468 | \end_inset
|
---|
| 2469 |
|
---|
| 2470 |
|
---|
| 2471 | \end_layout
|
---|
| 2472 |
|
---|
| 2473 | \begin_layout Standard
|
---|
| 2474 | \noindent
|
---|
| 2475 | Note also the following restrictions in the current version of SMMP:
|
---|
| 2476 | \end_layout
|
---|
| 2477 |
|
---|
| 2478 | \begin_layout Enumerate
|
---|
| 2479 | A single amino acid residue can not be simulated with the FLEX potential
|
---|
| 2480 | \end_layout
|
---|
| 2481 |
|
---|
| 2482 | \begin_layout Enumerate
|
---|
| 2483 | A protein must not start with a prolyl residue.
|
---|
| 2484 |
|
---|
| 2485 | \end_layout
|
---|
| 2486 |
|
---|
| 2487 | \begin_layout Section
|
---|
| 2488 | Libraries and Parameter Files
|
---|
| 2489 | \end_layout
|
---|
| 2490 |
|
---|
| 2491 | \begin_layout Standard
|
---|
| 2492 | The residues which can be used with each parameter set are described in
|
---|
| 2493 | files
|
---|
| 2494 | \shape italic
|
---|
| 2495 | lib.sh2, lib.sh3
|
---|
| 2496 | \shape default
|
---|
| 2497 | , and
|
---|
| 2498 | \shape italic
|
---|
| 2499 | lib.flex
|
---|
| 2500 | \shape default
|
---|
| 2501 | , respectively.
|
---|
| 2502 | The file
|
---|
| 2503 | \shape italic
|
---|
| 2504 | charges
|
---|
| 2505 | \shape default
|
---|
| 2506 | is needed for N- and C-terminal residues with FLEX parameters.
|
---|
| 2507 | The name of the directory, containing these 4 files should be given in
|
---|
| 2508 | string 'libdir', which is assigned in module MAIN.
|
---|
| 2509 | The choice between parameter sets for potentials ECEPP/2 and ECEPP/3 is
|
---|
| 2510 | done by the logical variable '
|
---|
| 2511 | \shape italic
|
---|
| 2512 | sh2
|
---|
| 2513 | \shape default
|
---|
| 2514 | '.
|
---|
| 2515 | The potential FLEX is set by the logical variable '
|
---|
| 2516 | \shape italic
|
---|
| 2517 | flex
|
---|
| 2518 | \shape default
|
---|
| 2519 | '.
|
---|
| 2520 | \end_layout
|
---|
| 2521 |
|
---|
| 2522 | \begin_layout Standard
|
---|
| 2523 | The amino acid residue libraries contain chemical and structural data for
|
---|
| 2524 | each residue according the IUPAC-IUB nomenclature.
|
---|
| 2525 | The library files consist of blocks of records with each block representing
|
---|
| 2526 | one residue.
|
---|
| 2527 | The first line in each block starts with a '#' and contains the name of
|
---|
| 2528 | the residue and its total number of atoms.
|
---|
| 2529 | Each following line within the block describes one atom.
|
---|
| 2530 | Listed are: its name, the bond length and the valence angle to construct
|
---|
| 2531 | this atom, the type and the name of corresponding torsion angle, the partial
|
---|
| 2532 | charge for the atom, the type of the atom, as well as the previous and
|
---|
| 2533 | the following atoms (max.
|
---|
| 2534 | 3), it is connected to.
|
---|
| 2535 | The atom and torsional parameters in the libraries are the same as in the
|
---|
| 2536 | original ECEPP/2/3 and FLEX potentials.
|
---|
| 2537 | However, it should be noted that SMMP has its own numeration of the atom
|
---|
| 2538 | types and the types of torsions (see [1,2] for more details).
|
---|
| 2539 | \end_layout
|
---|
| 2540 |
|
---|
| 2541 | \begin_layout Standard
|
---|
| 2542 | The arrays with the parameters for non bonded pairwise potentials (Van der
|
---|
| 2543 | Waals, hydrogen bonds, electrostatic) and the atomic solvation parameters
|
---|
| 2544 | are stored in the BLOCK DATA section of '
|
---|
| 2545 | \shape italic
|
---|
| 2546 | init_energy.f
|
---|
| 2547 | \shape default
|
---|
| 2548 | '.
|
---|
| 2549 | \end_layout
|
---|
| 2550 |
|
---|
| 2551 | \begin_layout Standard
|
---|
| 2552 | SMMP employs 9 different sets of atomic solvation parameters.
|
---|
| 2553 | We do not include references to the original works where these sets are
|
---|
| 2554 | defined in this document, since this manual is only a supplement to our
|
---|
| 2555 | articles
|
---|
| 2556 | \begin_inset LatexCommand cite
|
---|
| 2557 | key "Eisenmenger2001,Eisenmenger2006"
|
---|
| 2558 |
|
---|
| 2559 | \end_inset
|
---|
| 2560 |
|
---|
| 2561 | where all relevant references can be found.
|
---|
| 2562 | The set of solvation parameters chosen is indicated by the value of integer
|
---|
| 2563 | variable '
|
---|
| 2564 | \shape italic
|
---|
| 2565 | itysol
|
---|
| 2566 | \shape default
|
---|
| 2567 | ' in the MAIN module.
|
---|
| 2568 | If setting
|
---|
| 2569 | \shape italic
|
---|
| 2570 | itysol
|
---|
| 2571 | \shape default
|
---|
| 2572 | to a positive value between
|
---|
| 2573 | \shape italic
|
---|
| 2574 | 1
|
---|
| 2575 | \shape default
|
---|
| 2576 | and
|
---|
| 2577 | \shape italic
|
---|
| 2578 | 9
|
---|
| 2579 | \shape default
|
---|
| 2580 | in MAIN, the numerical method
|
---|
| 2581 | \shape italic
|
---|
| 2582 | enysol
|
---|
| 2583 | \shape default
|
---|
| 2584 | is applied to compute the solvation energy term.
|
---|
| 2585 | By choosing a negative integer value for
|
---|
| 2586 | \shape italic
|
---|
| 2587 | itysol
|
---|
| 2588 | \shape default
|
---|
| 2589 | from the interval
|
---|
| 2590 | \shape italic
|
---|
| 2591 | [-1,-9]
|
---|
| 2592 | \shape default
|
---|
| 2593 | , the analytical method
|
---|
| 2594 | \shape italic
|
---|
| 2595 | esolan
|
---|
| 2596 | \shape default
|
---|
| 2597 | is used to calculate the solvation energy.
|
---|
| 2598 | The tesselation points for numerically calculating the solvent accessible
|
---|
| 2599 | surface area have to be provided in an external file (named
|
---|
| 2600 | \shape italic
|
---|
| 2601 | tes.dat
|
---|
| 2602 | \shape default
|
---|
| 2603 | in our package) and read in during initialization of solvation parameters
|
---|
| 2604 | in
|
---|
| 2605 | \shape italic
|
---|
| 2606 | init_energy.f
|
---|
| 2607 | \shape default
|
---|
| 2608 | .
|
---|
| 2609 | \end_layout
|
---|
| 2610 |
|
---|
| 2611 | \begin_layout Section
|
---|
| 2612 | Input Files
|
---|
| 2613 | \end_layout
|
---|
| 2614 |
|
---|
| 2615 | \begin_layout Standard
|
---|
| 2616 | SMMP requires an input file that specifies the sequence of amino acid residues
|
---|
| 2617 | of the protein in plain ASCII-format.
|
---|
| 2618 |
|
---|
| 2619 | \end_layout
|
---|
| 2620 |
|
---|
| 2621 | \begin_layout Subsection
|
---|
| 2622 | PDB-File
|
---|
| 2623 | \begin_inset LatexCommand label
|
---|
| 2624 | name "sub:PDB-File"
|
---|
| 2625 |
|
---|
| 2626 | \end_inset
|
---|
| 2627 |
|
---|
| 2628 |
|
---|
| 2629 | \end_layout
|
---|
| 2630 |
|
---|
| 2631 | \begin_layout Standard
|
---|
| 2632 | Setting the variable '
|
---|
| 2633 | \shape italic
|
---|
| 2634 | iabin = 0
|
---|
| 2635 | \shape default
|
---|
| 2636 | ' in
|
---|
| 2637 | \shape italic
|
---|
| 2638 | main.f
|
---|
| 2639 | \shape default
|
---|
| 2640 | the sequence of amino acids is read from a PDB-file - the standard format
|
---|
| 2641 | in which protein structures are deposited in the Protein Data Bank.
|
---|
| 2642 | The atomic coordinates are also read from the PDB-file and can serve as
|
---|
| 2643 | a start configuration.
|
---|
| 2644 | However, the fixed bond lengths and angles in the standard geometry will
|
---|
| 2645 | slightly differ from the actual bond lengths and angles in the PDB-structure.
|
---|
| 2646 | Forcing the molecule into standard bonding geometry corresponding to a
|
---|
| 2647 | given potential may lead to un-physically high energies.
|
---|
| 2648 | Regularization through
|
---|
| 2649 | \shape italic
|
---|
| 2650 | regul.f
|
---|
| 2651 | \shape default
|
---|
| 2652 | allows to obtain an optimized structure with standard bonding geometry
|
---|
| 2653 | with low internal energy without differing significantly from the PDB structure.
|
---|
| 2654 |
|
---|
| 2655 | \end_layout
|
---|
| 2656 |
|
---|
| 2657 | \begin_layout Subsection
|
---|
| 2658 | Sequence File
|
---|
| 2659 | \begin_inset LatexCommand label
|
---|
| 2660 | name "sub:Sequence-File"
|
---|
| 2661 |
|
---|
| 2662 | \end_inset
|
---|
| 2663 |
|
---|
| 2664 |
|
---|
| 2665 | \end_layout
|
---|
| 2666 |
|
---|
| 2667 | \begin_layout Standard
|
---|
| 2668 | Setting `
|
---|
| 2669 | \shape italic
|
---|
| 2670 | iabin = 1
|
---|
| 2671 | \shape default
|
---|
| 2672 | ' the amino acid sequence is read from a separate sequence file.
|
---|
| 2673 | Its first line must start with a '#' and may contain the name for the molecule.
|
---|
| 2674 | The residues in the following lines should be named as in the library files
|
---|
| 2675 |
|
---|
| 2676 | \shape italic
|
---|
| 2677 | lib.sh2, lib.sh3
|
---|
| 2678 | \shape default
|
---|
| 2679 | , or
|
---|
| 2680 | \shape italic
|
---|
| 2681 | lib.flex
|
---|
| 2682 | \shape default
|
---|
| 2683 | .
|
---|
| 2684 | Residue names are not case-sensitive and should be separated from each
|
---|
| 2685 | other by at least one white space.
|
---|
| 2686 | \end_layout
|
---|
| 2687 |
|
---|
| 2688 | \begin_layout Standard
|
---|
| 2689 | Currently, the following residue types can be used in SMMP:
|
---|
| 2690 | \end_layout
|
---|
| 2691 |
|
---|
| 2692 | \begin_layout Enumerate
|
---|
| 2693 | Neutral:
|
---|
| 2694 | \newline
|
---|
| 2695 | ala, arg, asn, asp, cys, gln, glu, gly, his* ; hise* ; hyp*, ile,
|
---|
| 2696 | leu, lys, met, phe, pro* , ser, thr, trp, tyr, val
|
---|
| 2697 | \newline
|
---|
| 2698 | (where the residues
|
---|
| 2699 | marked by an asterix are characterized by:
|
---|
| 2700 | \newline
|
---|
| 2701 | his - hydrogen at N-delta atom
|
---|
| 2702 | \newline
|
---|
| 2703 |
|
---|
| 2704 | hise - hydrogen at N-epsilon atom
|
---|
| 2705 | \newline
|
---|
| 2706 | pro, hyp - down-puckering)
|
---|
| 2707 | \end_layout
|
---|
| 2708 |
|
---|
| 2709 | \begin_layout Enumerate
|
---|
| 2710 | Charged:
|
---|
| 2711 | \newline
|
---|
| 2712 | arg+, asp-, glu-, his+, lys+.
|
---|
| 2713 |
|
---|
| 2714 | \end_layout
|
---|
| 2715 |
|
---|
| 2716 | \begin_layout Enumerate
|
---|
| 2717 | Variants, only with ECEPP/3 parameters:
|
---|
| 2718 | \newline
|
---|
| 2719 | hypu, prou - up-puckering
|
---|
| 2720 | \newline
|
---|
| 2721 | cpro,
|
---|
| 2722 | cpru - cis-Pro with down-, up-puckering
|
---|
| 2723 | \newline
|
---|
| 2724 | pron, pro+ - N-terminal neutral,
|
---|
| 2725 | charged with respect to NH2+ Pro
|
---|
| 2726 | \end_layout
|
---|
| 2727 |
|
---|
| 2728 | \begin_layout Standard
|
---|
| 2729 | End-groups need to be specified in
|
---|
| 2730 | \shape italic
|
---|
| 2731 | main.f
|
---|
| 2732 | \shape default
|
---|
| 2733 | and are added through subroutine
|
---|
| 2734 | \shape italic
|
---|
| 2735 | addend
|
---|
| 2736 | \shape default
|
---|
| 2737 | to the N- and C-terminus, correspondingly.
|
---|
| 2738 | Possible values for the end groups are nh2 and nh3+ for the N terminal
|
---|
| 2739 | and cooh and coo- for the C terminal.
|
---|
| 2740 | Note, that the acetyl group ('
|
---|
| 2741 | \shape italic
|
---|
| 2742 | ace
|
---|
| 2743 | \shape default
|
---|
| 2744 | ') and N'methylamide ('
|
---|
| 2745 | \shape italic
|
---|
| 2746 | nme
|
---|
| 2747 | \shape default
|
---|
| 2748 | ') need to be added as
|
---|
| 2749 | \shape italic
|
---|
| 2750 | residues
|
---|
| 2751 | \shape default
|
---|
| 2752 | in the sequence file.
|
---|
| 2753 | In that case, input into '
|
---|
| 2754 | \shape italic
|
---|
| 2755 | addend
|
---|
| 2756 | \shape default
|
---|
| 2757 | ' will be ignored by SMMP.
|
---|
| 2758 | Note also, that at present, molecules with only one single residue cannot
|
---|
| 2759 | be simulated with the FLEX data set and the first residue should not be
|
---|
| 2760 | a prolyl residue.
|
---|
| 2761 | \end_layout
|
---|
| 2762 |
|
---|
| 2763 | \begin_layout Standard
|
---|
| 2764 | An example sequence file (provided with SMMP) may look as follows:
|
---|
| 2765 | \begin_inset ERT
|
---|
| 2766 | status collapsed
|
---|
| 2767 |
|
---|
| 2768 | \begin_layout Standard
|
---|
| 2769 |
|
---|
| 2770 |
|
---|
| 2771 | \backslash
|
---|
| 2772 | begin{verbatim}
|
---|
| 2773 | \end_layout
|
---|
| 2774 |
|
---|
| 2775 | \begin_layout Standard
|
---|
| 2776 |
|
---|
| 2777 | ------------------- enkefa.seq --------------------------
|
---|
| 2778 | \end_layout
|
---|
| 2779 |
|
---|
| 2780 | \begin_layout Standard
|
---|
| 2781 |
|
---|
| 2782 | # Met-Enkephalin
|
---|
| 2783 | \end_layout
|
---|
| 2784 |
|
---|
| 2785 | \begin_layout Standard
|
---|
| 2786 |
|
---|
| 2787 | Tyr Gly Gly Phe Met
|
---|
| 2788 | \end_layout
|
---|
| 2789 |
|
---|
| 2790 | \begin_layout Standard
|
---|
| 2791 |
|
---|
| 2792 | ---------------------------------------------------------
|
---|
| 2793 | \end_layout
|
---|
| 2794 |
|
---|
| 2795 | \begin_layout Standard
|
---|
| 2796 |
|
---|
| 2797 |
|
---|
| 2798 | \backslash
|
---|
| 2799 | end{verbatim}
|
---|
| 2800 | \end_layout
|
---|
| 2801 |
|
---|
| 2802 | \end_inset
|
---|
| 2803 |
|
---|
| 2804 |
|
---|
| 2805 | \end_layout
|
---|
| 2806 |
|
---|
| 2807 | \begin_layout Subsection
|
---|
| 2808 | Configuration File (Dihedrals)
|
---|
| 2809 | \begin_inset LatexCommand label
|
---|
| 2810 | name "sub:Configuration-File-(Dihedrals)"
|
---|
| 2811 |
|
---|
| 2812 | \end_inset
|
---|
| 2813 |
|
---|
| 2814 |
|
---|
| 2815 | \end_layout
|
---|
| 2816 |
|
---|
| 2817 | \begin_layout Standard
|
---|
| 2818 | With option '
|
---|
| 2819 | \shape italic
|
---|
| 2820 | iabin = 1
|
---|
| 2821 | \shape default
|
---|
| 2822 | ' SMMP allows to provide a designated start configuration by listing dihedral
|
---|
| 2823 | angles in a second input file.
|
---|
| 2824 | If no name of any configuration file is given (or the name of a non-existing
|
---|
| 2825 | file is entered), all variables retain their default values as defined
|
---|
| 2826 | in the libraries.
|
---|
| 2827 | \end_layout
|
---|
| 2828 |
|
---|
| 2829 | \begin_layout Standard
|
---|
| 2830 | This configuration file has to follow a fixed structure in which each line
|
---|
| 2831 | can be considered as a COMMAND for subroutine '
|
---|
| 2832 | \shape italic
|
---|
| 2833 | redvar
|
---|
| 2834 | \shape default
|
---|
| 2835 | '.
|
---|
| 2836 | The following syntax has to be used in each COMMAND: RESIDUE : VARIABLE
|
---|
| 2837 | : VALUE Hence, each line can consist of up to 3 FIELDS, separated by an
|
---|
| 2838 | ':'.
|
---|
| 2839 | In the first field the RESIDUE is selected through an INTEGER number which
|
---|
| 2840 | marks its position in the amino acid sequence.
|
---|
| 2841 | The second field should contain a string with the name of the VARIABLE,
|
---|
| 2842 | i.e.
|
---|
| 2843 | names the specific dihedral angle.
|
---|
| 2844 | The last field provides the value for the VARIABLE (a REAL number) and
|
---|
| 2845 | is mandatory.
|
---|
| 2846 | A symbol '&' following this number indicates that the variable will be
|
---|
| 2847 | fixed to that value throughout the whole simulation process.
|
---|
| 2848 | Spaces are not significant and are therefore ignored.
|
---|
| 2849 | Empty COMMANDS, as ' : : ', and empty lines or lines containing '#' are
|
---|
| 2850 | ignored.
|
---|
| 2851 | Missing fields are interpreted as 'for all':
|
---|
| 2852 | \begin_inset ERT
|
---|
| 2853 | status collapsed
|
---|
| 2854 |
|
---|
| 2855 | \begin_layout Standard
|
---|
| 2856 |
|
---|
| 2857 |
|
---|
| 2858 | \backslash
|
---|
| 2859 | begin{verbatim}
|
---|
| 2860 | \end_layout
|
---|
| 2861 |
|
---|
| 2862 | \begin_layout Standard
|
---|
| 2863 |
|
---|
| 2864 | 1 : phi : 180 Set phi of residue #1 to 180 degrees
|
---|
| 2865 | \end_layout
|
---|
| 2866 |
|
---|
| 2867 | \begin_layout Standard
|
---|
| 2868 |
|
---|
| 2869 | 1 : phi : 180& Keep phi of residue #1 fixed to 180 degrees
|
---|
| 2870 | \end_layout
|
---|
| 2871 |
|
---|
| 2872 | \begin_layout Standard
|
---|
| 2873 |
|
---|
| 2874 | phi : 180 Set phi of ALL residues to 180 degrees
|
---|
| 2875 | \end_layout
|
---|
| 2876 |
|
---|
| 2877 | \begin_layout Standard
|
---|
| 2878 |
|
---|
| 2879 | 180 Set all variables to 180 degrees
|
---|
| 2880 | \end_layout
|
---|
| 2881 |
|
---|
| 2882 | \begin_layout Standard
|
---|
| 2883 |
|
---|
| 2884 |
|
---|
| 2885 | \backslash
|
---|
| 2886 | end{verbatim}
|
---|
| 2887 | \end_layout
|
---|
| 2888 |
|
---|
| 2889 | \end_inset
|
---|
| 2890 |
|
---|
| 2891 | Several consecutive residues or variables can be indicated by ZONES of
|
---|
| 2892 | indices.
|
---|
| 2893 | Several NAMES can be indicated by wild-card ('*') and are case-sensitive:
|
---|
| 2894 |
|
---|
| 2895 | \begin_inset ERT
|
---|
| 2896 | status collapsed
|
---|
| 2897 |
|
---|
| 2898 | \begin_layout Standard
|
---|
| 2899 |
|
---|
| 2900 |
|
---|
| 2901 | \backslash
|
---|
| 2902 | begin{verbatim}
|
---|
| 2903 | \end_layout
|
---|
| 2904 |
|
---|
| 2905 | \begin_layout Standard
|
---|
| 2906 |
|
---|
| 2907 | 1-4 : phi : 180 Set 'phi' of residues #1,#2,#3, and #4 to 180 deg.
|
---|
| 2908 |
|
---|
| 2909 | \end_layout
|
---|
| 2910 |
|
---|
| 2911 | \begin_layout Standard
|
---|
| 2912 |
|
---|
| 2913 | 5 : x* : 60 Set all xi-angles of residue #5 to 60 deg.
|
---|
| 2914 | \end_layout
|
---|
| 2915 |
|
---|
| 2916 | \begin_layout Standard
|
---|
| 2917 |
|
---|
| 2918 |
|
---|
| 2919 | \backslash
|
---|
| 2920 | end{verbatim}
|
---|
| 2921 | \end_layout
|
---|
| 2922 |
|
---|
| 2923 | \end_inset
|
---|
| 2924 |
|
---|
| 2925 | Several NAMES or INDICES may be given in the same field, when separated
|
---|
| 2926 | by ','.
|
---|
| 2927 | Similarly, several commands may be given on the same line and must be separated
|
---|
| 2928 | by ';'
|
---|
| 2929 | \begin_inset ERT
|
---|
| 2930 | status collapsed
|
---|
| 2931 |
|
---|
| 2932 | \begin_layout Standard
|
---|
| 2933 |
|
---|
| 2934 |
|
---|
| 2935 | \backslash
|
---|
| 2936 | begin{verbatim}
|
---|
| 2937 | \end_layout
|
---|
| 2938 |
|
---|
| 2939 | \begin_layout Standard
|
---|
| 2940 |
|
---|
| 2941 | phi, psi : -30 Set all phi & psi to -30 deg.
|
---|
| 2942 |
|
---|
| 2943 | \end_layout
|
---|
| 2944 |
|
---|
| 2945 | \begin_layout Standard
|
---|
| 2946 |
|
---|
| 2947 | phi:-65; psi:-45 Set all phi=-65, all psi=-45
|
---|
| 2948 | \end_layout
|
---|
| 2949 |
|
---|
| 2950 | \begin_layout Standard
|
---|
| 2951 |
|
---|
| 2952 |
|
---|
| 2953 | \backslash
|
---|
| 2954 | end{verbatim}
|
---|
| 2955 | \end_layout
|
---|
| 2956 |
|
---|
| 2957 | \end_inset
|
---|
| 2958 |
|
---|
| 2959 | Note, that dihedral angles are defined slightly differently in SMMP than
|
---|
| 2960 | in standard ECEPP (residue index in parenthesis):
|
---|
| 2961 | \begin_inset ERT
|
---|
| 2962 | status open
|
---|
| 2963 |
|
---|
| 2964 | \begin_layout Standard
|
---|
| 2965 |
|
---|
| 2966 |
|
---|
| 2967 | \backslash
|
---|
| 2968 | begin{verbatim}
|
---|
| 2969 | \end_layout
|
---|
| 2970 |
|
---|
| 2971 | \begin_layout Standard
|
---|
| 2972 |
|
---|
| 2973 | - psi of the i-th residue = defined by N (i-1) - CA(i-1) - C (i-1) - N(i)
|
---|
| 2974 |
|
---|
| 2975 | \end_layout
|
---|
| 2976 |
|
---|
| 2977 | \begin_layout Standard
|
---|
| 2978 |
|
---|
| 2979 | - omg of the i-th residue = defined by CA(i-1) - C (i-1) - N (i) - CA(i)
|
---|
| 2980 |
|
---|
| 2981 | \end_layout
|
---|
| 2982 |
|
---|
| 2983 | \begin_layout Standard
|
---|
| 2984 |
|
---|
| 2985 | - phi for the i-th residue = defined by C (i-1) - N (i) - CA(i) - C(i)
|
---|
| 2986 |
|
---|
| 2987 | \end_layout
|
---|
| 2988 |
|
---|
| 2989 | \begin_layout Standard
|
---|
| 2990 |
|
---|
| 2991 |
|
---|
| 2992 | \backslash
|
---|
| 2993 | end{verbatim}
|
---|
| 2994 | \end_layout
|
---|
| 2995 |
|
---|
| 2996 | \end_inset
|
---|
| 2997 |
|
---|
| 2998 | except:
|
---|
| 2999 | \begin_inset ERT
|
---|
| 3000 | status open
|
---|
| 3001 |
|
---|
| 3002 | \begin_layout Standard
|
---|
| 3003 |
|
---|
| 3004 |
|
---|
| 3005 | \backslash
|
---|
| 3006 | begin{verbatim}
|
---|
| 3007 | \end_layout
|
---|
| 3008 |
|
---|
| 3009 | \begin_layout Standard
|
---|
| 3010 |
|
---|
| 3011 | phi for the 1st residue = defined by H1(1) - N (1) - CA(1) - C(1)
|
---|
| 3012 | \end_layout
|
---|
| 3013 |
|
---|
| 3014 | \begin_layout Standard
|
---|
| 3015 |
|
---|
| 3016 |
|
---|
| 3017 | \backslash
|
---|
| 3018 | end{verbatim}
|
---|
| 3019 | \end_layout
|
---|
| 3020 |
|
---|
| 3021 | \end_inset
|
---|
| 3022 |
|
---|
| 3023 | (H2-atom in the N-terminal NH2-group is added via dihedral 'H2-N-CA-C'=
|
---|
| 3024 | phi + 120)
|
---|
| 3025 | \end_layout
|
---|
| 3026 |
|
---|
| 3027 | \begin_layout Standard
|
---|
| 3028 | If a molecule consists of n residues then:
|
---|
| 3029 | \begin_inset ERT
|
---|
| 3030 | status open
|
---|
| 3031 |
|
---|
| 3032 | \begin_layout Standard
|
---|
| 3033 |
|
---|
| 3034 |
|
---|
| 3035 | \backslash
|
---|
| 3036 | begin{verbatim}
|
---|
| 3037 | \end_layout
|
---|
| 3038 |
|
---|
| 3039 | \begin_layout Standard
|
---|
| 3040 |
|
---|
| 3041 | - pst = defines dihedral N (n) - CA(n) - C (n) - Oxt(n)
|
---|
| 3042 | \end_layout
|
---|
| 3043 |
|
---|
| 3044 | \begin_layout Standard
|
---|
| 3045 |
|
---|
| 3046 | - omt = defines dihedral CA(n) - C (n) - Oxt(n) - Hxt(n)
|
---|
| 3047 | \end_layout
|
---|
| 3048 |
|
---|
| 3049 | \begin_layout Standard
|
---|
| 3050 |
|
---|
| 3051 |
|
---|
| 3052 | \backslash
|
---|
| 3053 | end{verbatim}
|
---|
| 3054 | \end_layout
|
---|
| 3055 |
|
---|
| 3056 | \end_inset
|
---|
| 3057 |
|
---|
| 3058 | (Oxt & Hxt comprise the hydroxyl of the C-terminal carboxyl group)
|
---|
| 3059 | \end_layout
|
---|
| 3060 |
|
---|
| 3061 | \begin_layout Standard
|
---|
| 3062 | The following example configuration file
|
---|
| 3063 | \shape italic
|
---|
| 3064 | enkefa.var
|
---|
| 3065 | \shape default
|
---|
| 3066 | is provided with the program and may be used with the sequence file
|
---|
| 3067 | \shape italic
|
---|
| 3068 | enkefa.seq
|
---|
| 3069 | \shape default
|
---|
| 3070 | :
|
---|
| 3071 | \begin_inset ERT
|
---|
| 3072 | status collapsed
|
---|
| 3073 |
|
---|
| 3074 | \begin_layout Standard
|
---|
| 3075 |
|
---|
| 3076 |
|
---|
| 3077 | \backslash
|
---|
| 3078 | begin{verbatim}
|
---|
| 3079 | \end_layout
|
---|
| 3080 |
|
---|
| 3081 | \begin_layout Standard
|
---|
| 3082 |
|
---|
| 3083 | ------------------- enkefa.var --------------------------
|
---|
| 3084 | \end_layout
|
---|
| 3085 |
|
---|
| 3086 | \begin_layout Standard
|
---|
| 3087 |
|
---|
| 3088 | 1 : phi : -86.24
|
---|
| 3089 | \end_layout
|
---|
| 3090 |
|
---|
| 3091 | \begin_layout Standard
|
---|
| 3092 |
|
---|
| 3093 | 1 : x1 : -172.59
|
---|
| 3094 | \end_layout
|
---|
| 3095 |
|
---|
| 3096 | \begin_layout Standard
|
---|
| 3097 |
|
---|
| 3098 | 1 : x2 : 78.71
|
---|
| 3099 | \end_layout
|
---|
| 3100 |
|
---|
| 3101 | \begin_layout Standard
|
---|
| 3102 |
|
---|
| 3103 | 1 : x6 : -165.88
|
---|
| 3104 | \end_layout
|
---|
| 3105 |
|
---|
| 3106 | \begin_layout Standard
|
---|
| 3107 |
|
---|
| 3108 | 2 : psi : 156.18
|
---|
| 3109 | \end_layout
|
---|
| 3110 |
|
---|
| 3111 | \begin_layout Standard
|
---|
| 3112 |
|
---|
| 3113 | 2 : omg : 180.00
|
---|
| 3114 | \end_layout
|
---|
| 3115 |
|
---|
| 3116 | \begin_layout Standard
|
---|
| 3117 |
|
---|
| 3118 | 2 : phi : -154.53
|
---|
| 3119 | \end_layout
|
---|
| 3120 |
|
---|
| 3121 | \begin_layout Standard
|
---|
| 3122 |
|
---|
| 3123 | 3 : psi : 83.64
|
---|
| 3124 | \end_layout
|
---|
| 3125 |
|
---|
| 3126 | \begin_layout Standard
|
---|
| 3127 |
|
---|
| 3128 | 3 : omg : 180.00
|
---|
| 3129 | \end_layout
|
---|
| 3130 |
|
---|
| 3131 | \begin_layout Standard
|
---|
| 3132 |
|
---|
| 3133 | 3 : phi : 83.66
|
---|
| 3134 | \end_layout
|
---|
| 3135 |
|
---|
| 3136 | \begin_layout Standard
|
---|
| 3137 |
|
---|
| 3138 | 4 : psi : -73.86
|
---|
| 3139 | \end_layout
|
---|
| 3140 |
|
---|
| 3141 | \begin_layout Standard
|
---|
| 3142 |
|
---|
| 3143 | 4 : omg : 180.00
|
---|
| 3144 | \end_layout
|
---|
| 3145 |
|
---|
| 3146 | \begin_layout Standard
|
---|
| 3147 |
|
---|
| 3148 | 4 : phi : -137.04
|
---|
| 3149 | \end_layout
|
---|
| 3150 |
|
---|
| 3151 | \begin_layout Standard
|
---|
| 3152 |
|
---|
| 3153 | 4 : x1 : 58.79
|
---|
| 3154 | \end_layout
|
---|
| 3155 |
|
---|
| 3156 | \begin_layout Standard
|
---|
| 3157 |
|
---|
| 3158 | 4 : x2 : 94.60
|
---|
| 3159 | \end_layout
|
---|
| 3160 |
|
---|
| 3161 | \begin_layout Standard
|
---|
| 3162 |
|
---|
| 3163 | 5 : psi : 19.33
|
---|
| 3164 | \end_layout
|
---|
| 3165 |
|
---|
| 3166 | \begin_layout Standard
|
---|
| 3167 |
|
---|
| 3168 | 5 : omg : -180.00
|
---|
| 3169 | \end_layout
|
---|
| 3170 |
|
---|
| 3171 | \begin_layout Standard
|
---|
| 3172 |
|
---|
| 3173 | 5 : phi : -163.63
|
---|
| 3174 | \end_layout
|
---|
| 3175 |
|
---|
| 3176 | \begin_layout Standard
|
---|
| 3177 |
|
---|
| 3178 | 5 : x1 : 52.76
|
---|
| 3179 | \end_layout
|
---|
| 3180 |
|
---|
| 3181 | \begin_layout Standard
|
---|
| 3182 |
|
---|
| 3183 | 5 : x2 : 175.28
|
---|
| 3184 | \end_layout
|
---|
| 3185 |
|
---|
| 3186 | \begin_layout Standard
|
---|
| 3187 |
|
---|
| 3188 | 5 : x3 : -179.83
|
---|
| 3189 | \end_layout
|
---|
| 3190 |
|
---|
| 3191 | \begin_layout Standard
|
---|
| 3192 |
|
---|
| 3193 | 5 : x4 : -58.57
|
---|
| 3194 | \end_layout
|
---|
| 3195 |
|
---|
| 3196 | \begin_layout Standard
|
---|
| 3197 |
|
---|
| 3198 | 5 : pst : 160.45
|
---|
| 3199 | \end_layout
|
---|
| 3200 |
|
---|
| 3201 | \begin_layout Standard
|
---|
| 3202 |
|
---|
| 3203 | 5 : omt : 180.00
|
---|
| 3204 | \end_layout
|
---|
| 3205 |
|
---|
| 3206 | \begin_layout Standard
|
---|
| 3207 |
|
---|
| 3208 | ---------------------------------------------------------
|
---|
| 3209 | \end_layout
|
---|
| 3210 |
|
---|
| 3211 | \begin_layout Standard
|
---|
| 3212 |
|
---|
| 3213 |
|
---|
| 3214 | \backslash
|
---|
| 3215 | end{verbatim}
|
---|
| 3216 | \end_layout
|
---|
| 3217 |
|
---|
| 3218 | \end_inset
|
---|
| 3219 |
|
---|
| 3220 |
|
---|
| 3221 | \end_layout
|
---|
| 3222 |
|
---|
| 3223 | \begin_layout Standard
|
---|
| 3224 | \begin_inset Float figure
|
---|
| 3225 | wide false
|
---|
| 3226 | sideways false
|
---|
| 3227 | status open
|
---|
| 3228 |
|
---|
| 3229 | \begin_layout Standard
|
---|
| 3230 | \align center
|
---|
| 3231 | \begin_inset Graphics
|
---|
| 3232 | filename atom_numbering.eps
|
---|
| 3233 | scaleBeforeRotation
|
---|
| 3234 |
|
---|
| 3235 | \end_inset
|
---|
| 3236 |
|
---|
| 3237 |
|
---|
| 3238 | \end_layout
|
---|
| 3239 |
|
---|
| 3240 | \begin_layout Standard
|
---|
| 3241 | \begin_inset Caption
|
---|
| 3242 |
|
---|
| 3243 | \begin_layout Standard
|
---|
| 3244 | \begin_inset LatexCommand label
|
---|
| 3245 | name "fig:Enumeration-of-atoms"
|
---|
| 3246 |
|
---|
| 3247 | \end_inset
|
---|
| 3248 |
|
---|
| 3249 | Enumeration of atoms in SMMP.
|
---|
| 3250 | Atoms are numbered starting from the N terminal of the protein.
|
---|
| 3251 | The terminal nitrogen has the index 1.
|
---|
| 3252 | Counting continues with the two attached hydrogens and then moves along
|
---|
| 3253 | the backbone.
|
---|
| 3254 | After the C
|
---|
| 3255 | \begin_inset Formula $_{\alpha}$
|
---|
| 3256 | \end_inset
|
---|
| 3257 |
|
---|
| 3258 | , we count along the side chain following a breadth-first scheme.
|
---|
| 3259 | Rings are enumerated counter clockwise.
|
---|
| 3260 |
|
---|
| 3261 | \end_layout
|
---|
| 3262 |
|
---|
| 3263 | \end_inset
|
---|
| 3264 |
|
---|
| 3265 |
|
---|
| 3266 | \end_layout
|
---|
| 3267 |
|
---|
| 3268 | \end_inset
|
---|
| 3269 |
|
---|
| 3270 |
|
---|
| 3271 | \end_layout
|
---|
| 3272 |
|
---|
| 3273 | \begin_layout Section
|
---|
| 3274 | Frequently used Functions and Subroutines
|
---|
| 3275 | \begin_inset LatexCommand label
|
---|
| 3276 | name "sec:Frequently-used-Functions"
|
---|
| 3277 |
|
---|
| 3278 | \end_inset
|
---|
| 3279 |
|
---|
| 3280 |
|
---|
| 3281 | \end_layout
|
---|
| 3282 |
|
---|
| 3283 | \begin_layout Subsection
|
---|
| 3284 | Task Subroutines
|
---|
| 3285 | \end_layout
|
---|
| 3286 |
|
---|
| 3287 | \begin_layout Standard
|
---|
| 3288 | In the following we describe some important simulation subroutines and their
|
---|
| 3289 | requisites.
|
---|
| 3290 | For more information see [1,2].
|
---|
| 3291 | Following the philosophy behind SMMP these routines are rather simple and
|
---|
| 3292 | may serve as templates which the user can modify according to his special
|
---|
| 3293 | needs.
|
---|
| 3294 |
|
---|
| 3295 | \end_layout
|
---|
| 3296 |
|
---|
| 3297 | \begin_layout Subsubsection
|
---|
| 3298 | Subroutine init_molecule(iabin, grpn, grpc, seqfile, varfile)
|
---|
| 3299 | \end_layout
|
---|
| 3300 |
|
---|
| 3301 | \begin_layout Standard
|
---|
| 3302 | (Usage: '
|
---|
| 3303 | \emph on
|
---|
| 3304 | call init_molecule(iabin, grpn, grpc, seqfile, varfile)')
|
---|
| 3305 | \end_layout
|
---|
| 3306 |
|
---|
| 3307 | \begin_layout Standard
|
---|
| 3308 | Initializes a new molecule and adds it to the system.
|
---|
| 3309 | The information is either read from a sequence (see
|
---|
| 3310 | \begin_inset LatexCommand ref
|
---|
| 3311 | reference "sub:Sequence-File"
|
---|
| 3312 |
|
---|
| 3313 | \end_inset
|
---|
| 3314 |
|
---|
| 3315 | ) and, optionally, a variable file (see
|
---|
| 3316 | \begin_inset LatexCommand ref
|
---|
| 3317 | reference "sub:Configuration-File-(Dihedrals)"
|
---|
| 3318 |
|
---|
| 3319 | \end_inset
|
---|
| 3320 |
|
---|
| 3321 | ) if
|
---|
| 3322 | \emph on
|
---|
| 3323 | iabin=1
|
---|
| 3324 | \emph default
|
---|
| 3325 | or from a pdb file (see
|
---|
| 3326 | \begin_inset LatexCommand ref
|
---|
| 3327 | reference "sub:PDB-File"
|
---|
| 3328 |
|
---|
| 3329 | \end_inset
|
---|
| 3330 |
|
---|
| 3331 | ) if
|
---|
| 3332 | \emph on
|
---|
| 3333 |
|
---|
| 3334 | \begin_inset Formula $iabin\neq1$
|
---|
| 3335 | \end_inset
|
---|
| 3336 |
|
---|
| 3337 |
|
---|
| 3338 | \emph default
|
---|
| 3339 | .
|
---|
| 3340 | If the molecule is read from a pdb file, the name of the file is given
|
---|
| 3341 | in
|
---|
| 3342 | \emph on
|
---|
| 3343 | seqfile
|
---|
| 3344 | \emph default
|
---|
| 3345 | .
|
---|
| 3346 | By repeatedly calling init_molecule, you can add several interacting molecules.
|
---|
| 3347 | The N-terminal group is determined by
|
---|
| 3348 | \emph on
|
---|
| 3349 | grpng
|
---|
| 3350 | \emph default
|
---|
| 3351 | and the C-terminal group
|
---|
| 3352 | \emph on
|
---|
| 3353 | grpc.
|
---|
| 3354 | \end_layout
|
---|
| 3355 |
|
---|
| 3356 | \begin_layout Subsubsection
|
---|
| 3357 | Subroutine REGUL(nml, iter, nsteps,
|
---|
| 3358 | \begin_inset Formula $\varepsilon$
|
---|
| 3359 | \end_inset
|
---|
| 3360 |
|
---|
| 3361 | )
|
---|
| 3362 | \begin_inset LatexCommand index
|
---|
| 3363 | name "REGUL"
|
---|
| 3364 |
|
---|
| 3365 | \end_inset
|
---|
| 3366 |
|
---|
| 3367 | (file regul.f)
|
---|
| 3368 | \end_layout
|
---|
| 3369 |
|
---|
| 3370 | \begin_layout Standard
|
---|
| 3371 | (Usage: '
|
---|
| 3372 | \shape italic
|
---|
| 3373 | call regul(nml, iter, nsteps,
|
---|
| 3374 | \begin_inset Formula $\varepsilon$
|
---|
| 3375 | \end_inset
|
---|
| 3376 |
|
---|
| 3377 | )
|
---|
| 3378 | \shape default
|
---|
| 3379 | ')
|
---|
| 3380 | \end_layout
|
---|
| 3381 |
|
---|
| 3382 | \begin_layout Standard
|
---|
| 3383 | For a given PDB-structure the actual bond lengths and bond angles generally
|
---|
| 3384 | differ from those in the standard geometry model assumed with the ECEPP
|
---|
| 3385 | or FLEX potential.
|
---|
| 3386 | This subroutine is applied to determine the configuration within the standard
|
---|
| 3387 | geometry that is as close as possible to a given PDB-structure with an
|
---|
| 3388 | energy as low as possible.
|
---|
| 3389 | This process of fitting a PDB structure into standard geometry is called
|
---|
| 3390 | regularization.
|
---|
| 3391 | '
|
---|
| 3392 | \shape italic
|
---|
| 3393 | regul
|
---|
| 3394 | \shape default
|
---|
| 3395 | ' requires the PDB-structure to be read into SMMP by setting '
|
---|
| 3396 | \shape italic
|
---|
| 3397 | iabin = 0
|
---|
| 3398 | \shape default
|
---|
| 3399 | ' in '
|
---|
| 3400 | \shape italic
|
---|
| 3401 | main
|
---|
| 3402 | \shape default
|
---|
| 3403 | '.
|
---|
| 3404 | With this option, `
|
---|
| 3405 | \shape italic
|
---|
| 3406 | init_molecule
|
---|
| 3407 | \shape default
|
---|
| 3408 | ' calls the subroutines `
|
---|
| 3409 | \shape italic
|
---|
| 3410 | pdbread
|
---|
| 3411 | \shape default
|
---|
| 3412 | ' and `
|
---|
| 3413 | \shape italic
|
---|
| 3414 | pdbvars
|
---|
| 3415 | \shape default
|
---|
| 3416 | ' that also to measure the dihedral angles in the PDB-structure.
|
---|
| 3417 | Using these dihedral angles a first model of the molecule is built using
|
---|
| 3418 | standard bonding geometry.
|
---|
| 3419 | Hence, '
|
---|
| 3420 | \shape italic
|
---|
| 3421 | regul
|
---|
| 3422 | \shape default
|
---|
| 3423 | ' has to be called AFTER '
|
---|
| 3424 | \shape italic
|
---|
| 3425 | init_molecule
|
---|
| 3426 | \shape default
|
---|
| 3427 | '.
|
---|
| 3428 | '
|
---|
| 3429 | \shape italic
|
---|
| 3430 | nml
|
---|
| 3431 | \shape default
|
---|
| 3432 | ' has to be set to 1 in the present version of SMMP.
|
---|
| 3433 | \end_layout
|
---|
| 3434 |
|
---|
| 3435 | \begin_layout Standard
|
---|
| 3436 | '
|
---|
| 3437 | \shape italic
|
---|
| 3438 | regul
|
---|
| 3439 | \shape default
|
---|
| 3440 | ' starts with a minimization of the initial structure using only the sum
|
---|
| 3441 | of squared distances between atom positions of the SMMP structure to the
|
---|
| 3442 | PDB-structure as
|
---|
| 3443 | \begin_inset Quotes erd
|
---|
| 3444 | \end_inset
|
---|
| 3445 |
|
---|
| 3446 | constraint energy
|
---|
| 3447 | \begin_inset Quotes erd
|
---|
| 3448 | \end_inset
|
---|
| 3449 |
|
---|
| 3450 | .
|
---|
| 3451 | After this initial step, a list of bad atom contacts, i.e.
|
---|
| 3452 | atoms with vdW-energy of more than 2 kcal/mol (as calculated by '
|
---|
| 3453 | \shape italic
|
---|
| 3454 | cnteny
|
---|
| 3455 | \shape default
|
---|
| 3456 | ') and the root-mean-square-deviation (rmsd) to the PDB-structure is printed
|
---|
| 3457 | out.
|
---|
| 3458 | In a second step, the physical energy is minimized, allowing only hydrogens
|
---|
| 3459 | to move, and bad contacts and the rmsd are evaluated, again.
|
---|
| 3460 | A number of iterations follow where a composite energy as the weighted
|
---|
| 3461 | sum of physical and constraint energy is minimized.
|
---|
| 3462 | In this iterations the weight of the constraint energy is successively
|
---|
| 3463 | lowered to zero, and that of the physical energy raised to one.
|
---|
| 3464 | At the end, the dihedral angles of the final structure are printed out
|
---|
| 3465 | together with its rmsd and list of remaining bad contacts.
|
---|
| 3466 |
|
---|
| 3467 | \end_layout
|
---|
| 3468 |
|
---|
| 3469 | \begin_layout Subsubsection
|
---|
| 3470 | Subroutine MINIM(imin, maxit,
|
---|
| 3471 | \begin_inset Formula $\varepsilon$
|
---|
| 3472 | \end_inset
|
---|
| 3473 |
|
---|
| 3474 | )
|
---|
| 3475 | \begin_inset LatexCommand index
|
---|
| 3476 | name "MINIM"
|
---|
| 3477 |
|
---|
| 3478 | \end_inset
|
---|
| 3479 |
|
---|
| 3480 | (file minim.f):
|
---|
| 3481 | \end_layout
|
---|
| 3482 |
|
---|
| 3483 | \begin_layout Standard
|
---|
| 3484 | (Usage:
|
---|
| 3485 | \shape italic
|
---|
| 3486 | 'call minim(imin
|
---|
| 3487 | \shape default
|
---|
| 3488 | , maxit,
|
---|
| 3489 | \begin_inset Formula $\varepsilon$
|
---|
| 3490 | \end_inset
|
---|
| 3491 |
|
---|
| 3492 | )')
|
---|
| 3493 | \newline
|
---|
| 3494 | This subroutine minimizes the current configuration of the molecule.
|
---|
| 3495 | It can be called from any point during the simulation once a configuration
|
---|
| 3496 | is defined.
|
---|
| 3497 | When calling this subroutine one needs to specify the type of minimizer
|
---|
| 3498 | through variable '
|
---|
| 3499 | \shape italic
|
---|
| 3500 | imin
|
---|
| 3501 | \shape default
|
---|
| 3502 | '.
|
---|
| 3503 | Setting '
|
---|
| 3504 | \shape italic
|
---|
| 3505 | imin = 1
|
---|
| 3506 | \shape default
|
---|
| 3507 | ' chooses a Quasi-Newton minimizer by calling '
|
---|
| 3508 | \shape italic
|
---|
| 3509 | minqsn
|
---|
| 3510 | \shape default
|
---|
| 3511 | ', '
|
---|
| 3512 | \shape italic
|
---|
| 3513 | imin = 2
|
---|
| 3514 | \shape default
|
---|
| 3515 | ' a Conjugate Gradient minimizer ('
|
---|
| 3516 | \shape italic
|
---|
| 3517 | mincjg
|
---|
| 3518 | \shape default
|
---|
| 3519 | ').
|
---|
| 3520 | The performance of these minimizers can be controlled by setting various
|
---|
| 3521 | parameters in MINIM.
|
---|
| 3522 | The two most commonly used ones, the accuracy ('
|
---|
| 3523 | \begin_inset Formula $\varepsilon$
|
---|
| 3524 | \end_inset
|
---|
| 3525 |
|
---|
| 3526 | ') and the total number of function calls 'mxit' are passed as arguments.
|
---|
| 3527 | \end_layout
|
---|
| 3528 |
|
---|
| 3529 | \begin_layout Subsubsection
|
---|
| 3530 | Subroutine CANON(nequi, nswp, nmes, temp, lrand)
|
---|
| 3531 | \begin_inset LatexCommand index
|
---|
| 3532 | name "CANON"
|
---|
| 3533 |
|
---|
| 3534 | \end_inset
|
---|
| 3535 |
|
---|
| 3536 | (file canon.f):
|
---|
| 3537 | \end_layout
|
---|
| 3538 |
|
---|
| 3539 | \begin_layout Standard
|
---|
| 3540 | (Usage: '
|
---|
| 3541 | \emph on
|
---|
| 3542 | call canon(nequi, nswp, nmes, temp, lrand)
|
---|
| 3543 | \emph default
|
---|
| 3544 | ')
|
---|
| 3545 | \newline
|
---|
| 3546 | The subroutine carries out a canonical simulation at temperature 'temp'.
|
---|
| 3547 | The simulation starts from a random configuration if the logical parameter
|
---|
| 3548 | 'lrand' is set to
|
---|
| 3549 | \shape italic
|
---|
| 3550 | .TRUE.
|
---|
| 3551 | \shape default
|
---|
| 3552 | .
|
---|
| 3553 | Otherwise the simulation starts from the current conformation of dihedral
|
---|
| 3554 | angles as stored in array 'vlvr'.
|
---|
| 3555 | One also has to set the number of Monte Carlo sweeps for the simulation
|
---|
| 3556 | 'nswp', and the equilibration 'nequi', as well as the number 'nmes' of
|
---|
| 3557 | Monte Carlo sweeps between measurements.
|
---|
| 3558 | Three output files are created: files `start.pdb' and 'final.pdb' are for
|
---|
| 3559 | storing the start and final configurations of the molecule, respectively,
|
---|
| 3560 | in a data format compatible with Protein Data Bank.
|
---|
| 3561 | The file 'time.d' contains the time series of some quantities.
|
---|
| 3562 | In our template we measure and store in this file the total energy 'eol';
|
---|
| 3563 | the radius-of-gyration `rgy' (by means of subroutine RGYR (
|
---|
| 3564 | \begin_inset LatexCommand ref
|
---|
| 3565 | reference "ite:Subroutine-RGYR"
|
---|
| 3566 |
|
---|
| 3567 | \end_inset
|
---|
| 3568 |
|
---|
| 3569 | )); the number of helical (
|
---|
| 3570 | \begin_inset Formula $\beta$
|
---|
| 3571 | \end_inset
|
---|
| 3572 |
|
---|
| 3573 | -sheet-like) residues 'nhel' ('nbet') and segments 'mhel' (`mbet') using
|
---|
| 3574 | subroutine HELIX (
|
---|
| 3575 | \begin_inset LatexCommand ref
|
---|
| 3576 | reference "ite:subroutine-HELIX"
|
---|
| 3577 |
|
---|
| 3578 | \end_inset
|
---|
| 3579 |
|
---|
| 3580 | ); and the number of hydrogen bonds 'mhb' calculated through subroutine
|
---|
| 3581 | HBOND (
|
---|
| 3582 | \begin_inset LatexCommand ref
|
---|
| 3583 | reference "ite:Subroutine-HBOND"
|
---|
| 3584 |
|
---|
| 3585 | \end_inset
|
---|
| 3586 |
|
---|
| 3587 | ).
|
---|
| 3588 |
|
---|
| 3589 | \end_layout
|
---|
| 3590 |
|
---|
| 3591 | \begin_layout Subsubsection
|
---|
| 3592 | Subroutine ANNEAL(nequi, nswp, nmes, tmax, tmin, lrand)
|
---|
| 3593 | \begin_inset LatexCommand index
|
---|
| 3594 | name "ANNEAL"
|
---|
| 3595 |
|
---|
| 3596 | \end_inset
|
---|
| 3597 |
|
---|
| 3598 | (file: anneal.f):
|
---|
| 3599 | \end_layout
|
---|
| 3600 |
|
---|
| 3601 | \begin_layout Standard
|
---|
| 3602 | (Usage: '
|
---|
| 3603 | \emph on
|
---|
| 3604 | call anneal(nequi, nswp, nmes, tmax, tmin, lrand)
|
---|
| 3605 | \emph default
|
---|
| 3606 | ')
|
---|
| 3607 | \end_layout
|
---|
| 3608 |
|
---|
| 3609 | \begin_layout Standard
|
---|
| 3610 | This subroutine allows for optimization of protein conformations by means
|
---|
| 3611 | of simulated annealing.
|
---|
| 3612 | When the logical parameter 'lrand' is set to
|
---|
| 3613 | \shape italic
|
---|
| 3614 | .TRUE.
|
---|
| 3615 |
|
---|
| 3616 | \shape default
|
---|
| 3617 | then the program will start from a random configuration.
|
---|
| 3618 | Otherwise, the annealing process will start from the current configuration
|
---|
| 3619 | as stored in the array 'vlvr'.
|
---|
| 3620 | You have to set the initial and final temperatures 'tmax' and 'tmin', the
|
---|
| 3621 | number of Monte Carlo sweeps for simulation nswp and equilibration 'nequi',
|
---|
| 3622 | and the number 'nmes' of Monte Carlo sweeps between measurements.
|
---|
| 3623 | Four output files are created in the same directory where the executable
|
---|
| 3624 | is running: three of them contain the start (start.pdb), the final (final.pdb)
|
---|
| 3625 | and the global minimum configuration (global.pdb), respectively, the 4th
|
---|
| 3626 | file (time.d) contains the time series of the simulation.
|
---|
| 3627 | In the presented template we measure and store in this file the actual
|
---|
| 3628 | temperature 'temp', the total energy 'eol', the radius-of-gyration 'rgy'
|
---|
| 3629 | (as calculated by subroutine RGYR) and the Zimmerman code (as character
|
---|
| 3630 | variable 'zimm') of the present configuration as obtained through subroutine
|
---|
| 3631 | ZIMMER.
|
---|
| 3632 |
|
---|
| 3633 | \end_layout
|
---|
| 3634 |
|
---|
| 3635 | \begin_layout Subsubsection
|
---|
| 3636 | Subroutine MULCAN_PAR(nsweep, nup, temp, kmin, kmax, binWidth, l_iter)
|
---|
| 3637 | \begin_inset LatexCommand index
|
---|
| 3638 | name "MULCANPAR"
|
---|
| 3639 |
|
---|
| 3640 | \end_inset
|
---|
| 3641 |
|
---|
| 3642 | (file mulcan_mod_par.f):
|
---|
| 3643 | \end_layout
|
---|
| 3644 |
|
---|
| 3645 | \begin_layout Standard
|
---|
| 3646 | This subroutine is part of the module
|
---|
| 3647 | \emph on
|
---|
| 3648 | multicanonical
|
---|
| 3649 | \emph default
|
---|
| 3650 | .
|
---|
| 3651 | To use the function include the module with
|
---|
| 3652 | \emph on
|
---|
| 3653 | use multicanonical
|
---|
| 3654 | \emph default
|
---|
| 3655 | in your main file.
|
---|
| 3656 | The subroutine calculates multicanonical weight factors and has two working
|
---|
| 3657 | modes.
|
---|
| 3658 | One is for improving the already existing set of multicanonical parameters
|
---|
| 3659 | through further iterations, and another to calculate them anew.
|
---|
| 3660 | In the first case the logical variable 'l_iter' is set to the value
|
---|
| 3661 | \shape italic
|
---|
| 3662 | .TRUE.
|
---|
| 3663 | \shape default
|
---|
| 3664 | .
|
---|
| 3665 | The histogram from a preliminary simulation as well as the existing values
|
---|
| 3666 | of the parameters are read from the file 'mpar_full.d'.
|
---|
| 3667 | In the second case ( 'l_iter' = .FALSE.) all arrays are initialized to zero.
|
---|
| 3668 | The values of 'kmin' and 'kmax' together with and the size of the energy
|
---|
| 3669 | bin 'ebinWidth' determine the energy range .
|
---|
| 3670 | The total number of Monte Carlo sweeps is given by 'nsweep', 'nup' is the
|
---|
| 3671 | number of Monte Carlo sweeps between updates of the multicanonical parameters,
|
---|
| 3672 | and 'temp' is the temperature of the initial canonical simulation.
|
---|
| 3673 | Every 'nup' sweeps the histogram of the preliminary simulation as well
|
---|
| 3674 | as the existing values of the parameters are written to the file 'mpar_full.d'.
|
---|
| 3675 | The final multicanonical parameters are written into the file 'muca.d'.
|
---|
| 3676 |
|
---|
| 3677 | \end_layout
|
---|
| 3678 |
|
---|
| 3679 | \begin_layout Subsubsection
|
---|
| 3680 | Subroutine MULCAN_SIM(nequi, nsweeps, nmes, nsave, kmin, kmax, binWidth,
|
---|
| 3681 | restart)
|
---|
| 3682 | \begin_inset LatexCommand index
|
---|
| 3683 | name "MULCANSIM"
|
---|
| 3684 |
|
---|
| 3685 | \end_inset
|
---|
| 3686 |
|
---|
| 3687 | (file mulcan_sim.f):
|
---|
| 3688 | \end_layout
|
---|
| 3689 |
|
---|
| 3690 | \begin_layout Standard
|
---|
| 3691 | This subroutine performs a Monte Carlo simulation of a protein using multicanoni
|
---|
| 3692 | cal weights.
|
---|
| 3693 | Information necessary for a re-start are saved after every 'nsave' Monte
|
---|
| 3694 | Carlo moves into the file 'start.d'.
|
---|
| 3695 | You can restart a simulation by setting 'restart'=.TRUE.
|
---|
| 3696 | otherwise the simulation starts from a random configuration.
|
---|
| 3697 | Parameters 'binWidth', 'kmin', and 'kmax' set the energy-bin size and the
|
---|
| 3698 | lower and upper limits of the energy interval, within which the multicanonical
|
---|
| 3699 | parameters were defined (see MULCAN_PAR).
|
---|
| 3700 | These parameters are read from the file 'muca.d' and have to be the same
|
---|
| 3701 | as the ones used in MULCAN_PAR to generate the multicanonical weights.
|
---|
| 3702 | The total number of Monte Carlo sweeps is 'nsweep', the number of Monte
|
---|
| 3703 | Carlo sweeps needed for equilibration is 'nequi', and the interval between
|
---|
| 3704 | successive measurements is 'nmes'.
|
---|
| 3705 | In our example the output goes to 'time.d', in which the time series of
|
---|
| 3706 | the simulation is written.
|
---|
| 3707 | Measured quantities are the total potential energy 'eol', the number of
|
---|
| 3708 | contacts 'nhx' and the number of native contacts 'nhy'.
|
---|
| 3709 | The latter number counts the contacts that are the same in the present
|
---|
| 3710 | configuration and the target structure.
|
---|
| 3711 | Also measured is the Hamming distance 'dham' between the present and the
|
---|
| 3712 | target configuration.
|
---|
| 3713 | The latter three quantities are calculated by the subroutine CONTACTS.
|
---|
| 3714 | The contact map needs to be initialized before calling mulcan_sim., for
|
---|
| 3715 | example with the following code:
|
---|
| 3716 | \begin_inset ERT
|
---|
| 3717 | status collapsed
|
---|
| 3718 |
|
---|
| 3719 | \begin_layout Standard
|
---|
| 3720 |
|
---|
| 3721 |
|
---|
| 3722 | \backslash
|
---|
| 3723 | begin{verbatim}
|
---|
| 3724 | \end_layout
|
---|
| 3725 |
|
---|
| 3726 | \begin_layout Standard
|
---|
| 3727 |
|
---|
| 3728 | open(9,file='enkefa.ref')
|
---|
| 3729 | \end_layout
|
---|
| 3730 |
|
---|
| 3731 | \begin_layout Standard
|
---|
| 3732 |
|
---|
| 3733 | nresi=irsml2(1)-irsml1(1) + 1
|
---|
| 3734 | \end_layout
|
---|
| 3735 |
|
---|
| 3736 | \begin_layout Standard
|
---|
| 3737 |
|
---|
| 3738 | ! nresi: Number of residues
|
---|
| 3739 | \end_layout
|
---|
| 3740 |
|
---|
| 3741 | \begin_layout Standard
|
---|
| 3742 |
|
---|
| 3743 | ! Read reference contact map
|
---|
| 3744 | \end_layout
|
---|
| 3745 |
|
---|
| 3746 | \begin_layout Standard
|
---|
| 3747 |
|
---|
| 3748 | nci = 0
|
---|
| 3749 | \end_layout
|
---|
| 3750 |
|
---|
| 3751 | \begin_layout Standard
|
---|
| 3752 |
|
---|
| 3753 | do i=1,nresi
|
---|
| 3754 | \end_layout
|
---|
| 3755 |
|
---|
| 3756 | \begin_layout Standard
|
---|
| 3757 |
|
---|
| 3758 | read(9,*) (iref(i,j) , j=1,nresi)
|
---|
| 3759 | \end_layout
|
---|
| 3760 |
|
---|
| 3761 | \begin_layout Standard
|
---|
| 3762 |
|
---|
| 3763 | end do
|
---|
| 3764 | \end_layout
|
---|
| 3765 |
|
---|
| 3766 | \begin_layout Standard
|
---|
| 3767 |
|
---|
| 3768 | do i=1,nresi
|
---|
| 3769 | \end_layout
|
---|
| 3770 |
|
---|
| 3771 | \begin_layout Standard
|
---|
| 3772 |
|
---|
| 3773 | do j=nresi,i+3,-1
|
---|
| 3774 | \end_layout
|
---|
| 3775 |
|
---|
| 3776 | \begin_layout Standard
|
---|
| 3777 |
|
---|
| 3778 | if(iref(i,j).eq.1) nci = nci + 1
|
---|
| 3779 | \end_layout
|
---|
| 3780 |
|
---|
| 3781 | \begin_layout Standard
|
---|
| 3782 |
|
---|
| 3783 | end do
|
---|
| 3784 | \end_layout
|
---|
| 3785 |
|
---|
| 3786 | \begin_layout Standard
|
---|
| 3787 |
|
---|
| 3788 | end do
|
---|
| 3789 | \end_layout
|
---|
| 3790 |
|
---|
| 3791 | \begin_layout Standard
|
---|
| 3792 |
|
---|
| 3793 | write(*,*) 'Number of contacts in reference conformation:',nci
|
---|
| 3794 | \end_layout
|
---|
| 3795 |
|
---|
| 3796 | \begin_layout Standard
|
---|
| 3797 |
|
---|
| 3798 |
|
---|
| 3799 | \backslash
|
---|
| 3800 | end{verbatim}
|
---|
| 3801 | \end_layout
|
---|
| 3802 |
|
---|
| 3803 | \end_inset
|
---|
| 3804 |
|
---|
| 3805 |
|
---|
| 3806 | \end_layout
|
---|
| 3807 |
|
---|
| 3808 | \begin_layout Subsubsection
|
---|
| 3809 | Subroutine PARTEM_S
|
---|
| 3810 | \begin_inset LatexCommand index
|
---|
| 3811 | name "PARTEMS"
|
---|
| 3812 |
|
---|
| 3813 | \end_inset
|
---|
| 3814 |
|
---|
| 3815 |
|
---|
| 3816 | \end_layout
|
---|
| 3817 |
|
---|
| 3818 | \begin_layout Standard
|
---|
| 3819 | (file partem_s.f):
|
---|
| 3820 | \end_layout
|
---|
| 3821 |
|
---|
| 3822 | \begin_layout Standard
|
---|
| 3823 | This parameterless subroutine is designed to simulate a protein by means
|
---|
| 3824 | of the parallel tempering technique on a single processor.
|
---|
| 3825 | Before running a parallel tempering simulation using PARTEM_S one has to
|
---|
| 3826 | set the following variables in this subroutine: the number of replicas
|
---|
| 3827 | ('no') and the initial temperatures on each replica (array 'temp(no)');
|
---|
| 3828 | the sum of the number of degrees of freedom over all replicas ('nvrmax');
|
---|
| 3829 | the number of Monte Carlo sweeps at equilibration ('nequi') and the number
|
---|
| 3830 | of Monte Carlo sweeps between measurements ('nmes').
|
---|
| 3831 | Except for re-starts, the logical variable 'lstart' should be set to .FALSE.,
|
---|
| 3832 | in which case all dihedral angles are set to random values.
|
---|
| 3833 | At the end of the simulation all dihedral angles are stored in the file
|
---|
| 3834 | 'startconf.d', from which the program reads its start configuration, if
|
---|
| 3835 | 'lstart=.TRUE.'.
|
---|
| 3836 | In the simulation, measurements are made every 'nmes' Monte Carlo sweeps.
|
---|
| 3837 | In our template, we measure for each replica the radius-of gyration 'rgy'
|
---|
| 3838 | and the end-to-end distance 'ee' by means of subroutine RGYR and write
|
---|
| 3839 | both values together with the temperature 'temp0' , total energy 'energy',
|
---|
| 3840 | Monte Carlo time 'nsw', and the index of the replicas 'k1' to an output
|
---|
| 3841 | file 'time.d'.
|
---|
| 3842 |
|
---|
| 3843 | \end_layout
|
---|
| 3844 |
|
---|
| 3845 | \begin_layout Subsubsection
|
---|
| 3846 | PMAIN and subroutine PARTEM_P
|
---|
| 3847 | \begin_inset LatexCommand index
|
---|
| 3848 | name "PARTEMP"
|
---|
| 3849 |
|
---|
| 3850 | \end_inset
|
---|
| 3851 |
|
---|
| 3852 | (files pmain.f and partem_p.f)
|
---|
| 3853 | \end_layout
|
---|
| 3854 |
|
---|
| 3855 | \begin_layout Standard
|
---|
| 3856 | (Usage: '
|
---|
| 3857 | \emph on
|
---|
| 3858 | call partem_p(no, nequi, nswp, nmes, newsta, switch)
|
---|
| 3859 | \emph default
|
---|
| 3860 | ')
|
---|
| 3861 | \end_layout
|
---|
| 3862 |
|
---|
| 3863 | \begin_layout Standard
|
---|
| 3864 | PMAIN and PARTEM_P are used for parallel tempering simulations on a parallel
|
---|
| 3865 | computer with 'no' nodes.
|
---|
| 3866 | PMAIN replaces MAIN in this case.
|
---|
| 3867 | Both PMAIN and PARTEM_P utilize the MPI message-passing routines.
|
---|
| 3868 | The number of nodes 'no' has to be set in the main program and equals the
|
---|
| 3869 | number of replicas in the parallel tempering method.
|
---|
| 3870 | In addition, one has to pass the following variables to PARTEM_P: the number
|
---|
| 3871 | of Monte Carlo sweeps for equilibration nequi and the total simulation
|
---|
| 3872 | nswp; and the number of Monte Carlo sweeps between measurements ('nmes').
|
---|
| 3873 | Except for restarts the logical variable 'newsta' should be set to .FALSE..
|
---|
| 3874 | If newsta is .TRUE., switch determines the starting configuration.
|
---|
| 3875 | If switch=1, all dihedral angles are set to the random values.
|
---|
| 3876 | If switch=-1, all dihedral angles are set to 180.
|
---|
| 3877 | If switch=0, the configuration remains unchanged.
|
---|
| 3878 | At the end of the simulation all dihedral angles are stored in the file
|
---|
| 3879 | 'par_R.in', from which the program reads its start configurations if 'newsta=.TRU
|
---|
| 3880 | E.'.
|
---|
| 3881 | Before running the program one has to prepare the file 'temp.d' with 'no'
|
---|
| 3882 | lines.
|
---|
| 3883 | Each line lists the index of replica 'j' and its temperature 'temp'.
|
---|
| 3884 | In our template we measure every 'nmes' Monte Carlo sweeps for each replica
|
---|
| 3885 | a number of quantities: the radius of gyration 'rgy', the number of residues
|
---|
| 3886 | 'nhel' and segments 'mhel' in an
|
---|
| 3887 | \begin_inset Formula $\alpha$
|
---|
| 3888 | \end_inset
|
---|
| 3889 |
|
---|
| 3890 | -helix, the number of residues in a
|
---|
| 3891 | \begin_inset Formula $\beta$
|
---|
| 3892 | \end_inset
|
---|
| 3893 |
|
---|
| 3894 | -sheet 'nbet' and the number of such segments 'mbet', the number of hydrogen
|
---|
| 3895 | bonds 'mhb', and the number of contacts 'nctot' and native contacts 'ncnat'.
|
---|
| 3896 | The latter number counts the contacts which are same in the present configurati
|
---|
| 3897 | on and in the target structure For this, one has to prepare in advance the
|
---|
| 3898 | file 'reference.d' with the contact matrix of the target structure.
|
---|
| 3899 | All measured quantities are written together with energy, temperature and
|
---|
| 3900 | the index of the corresponding replica in the file 'ts.d'.
|
---|
| 3901 | At the end of the simulation the average energy and specific heat for each
|
---|
| 3902 | temperature/replica and the acceptance rate of replica-exchange moves are
|
---|
| 3903 | written to standard output.
|
---|
| 3904 |
|
---|
| 3905 | \end_layout
|
---|
| 3906 |
|
---|
| 3907 | \begin_layout Subsection
|
---|
| 3908 | Useful Subroutines
|
---|
| 3909 | \end_layout
|
---|
| 3910 |
|
---|
| 3911 | \begin_layout Subsubsection
|
---|
| 3912 | Subroutine CONTACTS
|
---|
| 3913 | \begin_inset LatexCommand index
|
---|
| 3914 | name "CONTACTS"
|
---|
| 3915 |
|
---|
| 3916 | \end_inset
|
---|
| 3917 |
|
---|
| 3918 |
|
---|
| 3919 | \end_layout
|
---|
| 3920 |
|
---|
| 3921 | \begin_layout Standard
|
---|
| 3922 | (Usage:
|
---|
| 3923 | \shape italic
|
---|
| 3924 | call contacts(ncn,nham2,dham)
|
---|
| 3925 | \shape default
|
---|
| 3926 | ):
|
---|
| 3927 | \end_layout
|
---|
| 3928 |
|
---|
| 3929 | \begin_layout Standard
|
---|
| 3930 | This subroutine calculates the matrix of the van-der-Waals contacts between
|
---|
| 3931 | C
|
---|
| 3932 | \begin_inset Formula $^{\alpha}$
|
---|
| 3933 | \end_inset
|
---|
| 3934 |
|
---|
| 3935 | -atoms for a given configuration.
|
---|
| 3936 | 'ncn' is the total number of such contacts, 'nham2' the number of native
|
---|
| 3937 | contacts (i.e.
|
---|
| 3938 | such con- tacts which are the same in the present configuration and the
|
---|
| 3939 | reference configuration), and the Hamming distance 'dham' between the present
|
---|
| 3940 | and the target configuration.
|
---|
| 3941 |
|
---|
| 3942 | \end_layout
|
---|
| 3943 |
|
---|
| 3944 | \begin_layout Subsubsection
|
---|
| 3945 | Subroutine CNTENY
|
---|
| 3946 | \begin_inset LatexCommand index
|
---|
| 3947 | name "CNTENY"
|
---|
| 3948 |
|
---|
| 3949 | \end_inset
|
---|
| 3950 |
|
---|
| 3951 | :
|
---|
| 3952 | \end_layout
|
---|
| 3953 |
|
---|
| 3954 | \begin_layout Standard
|
---|
| 3955 | (Usage:
|
---|
| 3956 | \emph on
|
---|
| 3957 | call cnteny(nml)
|
---|
| 3958 | \emph default
|
---|
| 3959 | )
|
---|
| 3960 | \end_layout
|
---|
| 3961 |
|
---|
| 3962 | \begin_layout Standard
|
---|
| 3963 | The subroutine '
|
---|
| 3964 | \emph on
|
---|
| 3965 | cnteny
|
---|
| 3966 | \emph default
|
---|
| 3967 | ' displays a list of heavy atoms in molecule '
|
---|
| 3968 | \emph on
|
---|
| 3969 | nml
|
---|
| 3970 | \emph default
|
---|
| 3971 | ' that have a contact energy of more than 2 kcal/mol.
|
---|
| 3972 | If one sets the parameter '
|
---|
| 3973 | \emph on
|
---|
| 3974 | ieyel = 0
|
---|
| 3975 | \emph default
|
---|
| 3976 | ' in '
|
---|
| 3977 | \emph on
|
---|
| 3978 | cnteny
|
---|
| 3979 | \emph default
|
---|
| 3980 | ' the the contact energy is calculated with the van-der-Waals energy term,
|
---|
| 3981 | only.
|
---|
| 3982 | Setting '
|
---|
| 3983 | \emph on
|
---|
| 3984 | ieyel = 1
|
---|
| 3985 | \emph default
|
---|
| 3986 | ' additionally includes the electrostatic energy into the contact energy,
|
---|
| 3987 | and bad contacts are displayed if this energy exceeds a value of 10 kcal/mol
|
---|
| 3988 | for an atom.
|
---|
| 3989 |
|
---|
| 3990 | \end_layout
|
---|
| 3991 |
|
---|
| 3992 | \begin_layout Subsubsection
|
---|
| 3993 | Functions ENERGY
|
---|
| 3994 | \begin_inset LatexCommand index
|
---|
| 3995 | name "ENERGY"
|
---|
| 3996 |
|
---|
| 3997 | \end_inset
|
---|
| 3998 |
|
---|
| 3999 | , ENYSHE
|
---|
| 4000 | \begin_inset LatexCommand index
|
---|
| 4001 | name "ENYSHE"
|
---|
| 4002 |
|
---|
| 4003 | \end_inset
|
---|
| 4004 |
|
---|
| 4005 | , ENYFLX
|
---|
| 4006 | \begin_inset LatexCommand index
|
---|
| 4007 | name "ENYFLX"
|
---|
| 4008 |
|
---|
| 4009 | \end_inset
|
---|
| 4010 |
|
---|
| 4011 | , ENYSOL
|
---|
| 4012 | \begin_inset LatexCommand index
|
---|
| 4013 | name "ENYSOL"
|
---|
| 4014 |
|
---|
| 4015 | \end_inset
|
---|
| 4016 |
|
---|
| 4017 | , ESOLAN
|
---|
| 4018 | \begin_inset LatexCommand index
|
---|
| 4019 | name "ESOLAN"
|
---|
| 4020 |
|
---|
| 4021 | \end_inset
|
---|
| 4022 |
|
---|
| 4023 | , and ENYREG
|
---|
| 4024 | \begin_inset LatexCommand index
|
---|
| 4025 | name "ENYREG"
|
---|
| 4026 |
|
---|
| 4027 | \end_inset
|
---|
| 4028 |
|
---|
| 4029 | :
|
---|
| 4030 | \end_layout
|
---|
| 4031 |
|
---|
| 4032 | \begin_layout Standard
|
---|
| 4033 | (Usage:
|
---|
| 4034 | \shape italic
|
---|
| 4035 | eny = energy()
|
---|
| 4036 | \shape default
|
---|
| 4037 | )
|
---|
| 4038 | \newline
|
---|
| 4039 | The real*8 function `
|
---|
| 4040 | \shape italic
|
---|
| 4041 | energy
|
---|
| 4042 | \shape default
|
---|
| 4043 | ' is a wrapping function that calculates the energy of a given configuration.
|
---|
| 4044 | Depending on the choice of parameters '
|
---|
| 4045 | \shape italic
|
---|
| 4046 | flex
|
---|
| 4047 | \shape default
|
---|
| 4048 | ', '
|
---|
| 4049 | \shape italic
|
---|
| 4050 | sh2
|
---|
| 4051 | \shape default
|
---|
| 4052 | ', '
|
---|
| 4053 | \shape italic
|
---|
| 4054 | itysol
|
---|
| 4055 | \shape default
|
---|
| 4056 | ' and '
|
---|
| 4057 | \shape italic
|
---|
| 4058 | ireg
|
---|
| 4059 | \shape default
|
---|
| 4060 | ' in '
|
---|
| 4061 | \shape italic
|
---|
| 4062 | main
|
---|
| 4063 | \shape default
|
---|
| 4064 | ' ('
|
---|
| 4065 | \shape italic
|
---|
| 4066 | pmain
|
---|
| 4067 | \shape default
|
---|
| 4068 | ') the `vacuum' energy of the protein is calculated by the functions '
|
---|
| 4069 | \shape italic
|
---|
| 4070 | enyshe
|
---|
| 4071 | \shape default
|
---|
| 4072 | ' (ECEPP/2 or ECEPP/3), or '
|
---|
| 4073 | \shape italic
|
---|
| 4074 | enyflex
|
---|
| 4075 | \shape default
|
---|
| 4076 | ' (FLEX), and the solvation energy using the solvent accessible area method
|
---|
| 4077 | with '
|
---|
| 4078 | \shape italic
|
---|
| 4079 | enysol
|
---|
| 4080 | \shape default
|
---|
| 4081 | ' (approximate, but fast estimation of the solvated area) or '
|
---|
| 4082 | \shape italic
|
---|
| 4083 | esolan
|
---|
| 4084 | \shape default
|
---|
| 4085 | ' (analytical, but slower calculation of the area).
|
---|
| 4086 | '
|
---|
| 4087 | \shape italic
|
---|
| 4088 | enyreg
|
---|
| 4089 | \shape default
|
---|
| 4090 | ' calculates the constraint energy term needed during regularization of
|
---|
| 4091 | PDB-structures.
|
---|
| 4092 | '
|
---|
| 4093 | \shape italic
|
---|
| 4094 | energy
|
---|
| 4095 | \shape default
|
---|
| 4096 | ' returns the sum of these energy terms as selected by the parameters in
|
---|
| 4097 | the 'main'-module.
|
---|
| 4098 |
|
---|
| 4099 | \end_layout
|
---|
| 4100 |
|
---|
| 4101 | \begin_layout Subsubsection
|
---|
| 4102 | Subroutine GRADIENT
|
---|
| 4103 | \begin_inset LatexCommand index
|
---|
| 4104 | name "GRADIENT"
|
---|
| 4105 |
|
---|
| 4106 | \end_inset
|
---|
| 4107 |
|
---|
| 4108 | , OPESHE
|
---|
| 4109 | \begin_inset LatexCommand index
|
---|
| 4110 | name "OPESHE"
|
---|
| 4111 |
|
---|
| 4112 | \end_inset
|
---|
| 4113 |
|
---|
| 4114 | , OPEFLX
|
---|
| 4115 | \begin_inset LatexCommand index
|
---|
| 4116 | name "OPEFLX"
|
---|
| 4117 |
|
---|
| 4118 | \end_inset
|
---|
| 4119 |
|
---|
| 4120 | , OPESOL
|
---|
| 4121 | \begin_inset LatexCommand index
|
---|
| 4122 | name "OPESOL"
|
---|
| 4123 |
|
---|
| 4124 | \end_inset
|
---|
| 4125 |
|
---|
| 4126 | , and OPEREG
|
---|
| 4127 | \begin_inset LatexCommand index
|
---|
| 4128 | name "OPEREG"
|
---|
| 4129 |
|
---|
| 4130 | \end_inset
|
---|
| 4131 |
|
---|
| 4132 | :
|
---|
| 4133 | \end_layout
|
---|
| 4134 |
|
---|
| 4135 | \begin_layout Standard
|
---|
| 4136 | (Usage:
|
---|
| 4137 | \shape italic
|
---|
| 4138 | call gradient()
|
---|
| 4139 | \shape default
|
---|
| 4140 | )
|
---|
| 4141 | \newline
|
---|
| 4142 | The wrapping subroutine '
|
---|
| 4143 | \shape italic
|
---|
| 4144 | gradient
|
---|
| 4145 | \shape default
|
---|
| 4146 | ' calculates the energy and partial derivatives (with respect to internal
|
---|
| 4147 | degrees of freedom) for a given protein configuration.
|
---|
| 4148 | Depending on the choice of parameters '
|
---|
| 4149 | \shape italic
|
---|
| 4150 | flex
|
---|
| 4151 | \shape default
|
---|
| 4152 | ', '
|
---|
| 4153 | \shape italic
|
---|
| 4154 | sh2
|
---|
| 4155 | \shape default
|
---|
| 4156 | ', '
|
---|
| 4157 | \shape italic
|
---|
| 4158 | itysol
|
---|
| 4159 | \shape default
|
---|
| 4160 | ', and '
|
---|
| 4161 | \shape italic
|
---|
| 4162 | ireg
|
---|
| 4163 | \shape default
|
---|
| 4164 | ', the subroutines '
|
---|
| 4165 | \shape italic
|
---|
| 4166 | opeshe
|
---|
| 4167 | \shape default
|
---|
| 4168 | ' (ECEPP/2 or ECEPP/3), '
|
---|
| 4169 | \shape italic
|
---|
| 4170 | opeflx
|
---|
| 4171 | \shape default
|
---|
| 4172 | ' (FLEX), '
|
---|
| 4173 | \shape italic
|
---|
| 4174 | opesol
|
---|
| 4175 | \shape default
|
---|
| 4176 | ' (solvent accessible surface area) and/or '
|
---|
| 4177 | \shape italic
|
---|
| 4178 | opereg
|
---|
| 4179 | \shape default
|
---|
| 4180 | ' (constraint energy term during regularization of PDB structures) are selected
|
---|
| 4181 | and contribute to the total energy and its gradient that is calculated.
|
---|
| 4182 |
|
---|
| 4183 | \end_layout
|
---|
| 4184 |
|
---|
| 4185 | \begin_layout Subsubsection
|
---|
| 4186 | \begin_inset LatexCommand label
|
---|
| 4187 | name "ite:Subroutine-HBOND"
|
---|
| 4188 |
|
---|
| 4189 | \end_inset
|
---|
| 4190 |
|
---|
| 4191 | Subroutine HBOND
|
---|
| 4192 | \begin_inset LatexCommand index
|
---|
| 4193 | name "HBOND"
|
---|
| 4194 |
|
---|
| 4195 | \end_inset
|
---|
| 4196 |
|
---|
| 4197 |
|
---|
| 4198 | \end_layout
|
---|
| 4199 |
|
---|
| 4200 | \begin_layout Standard
|
---|
| 4201 | (Usage:
|
---|
| 4202 | \shape italic
|
---|
| 4203 | call hbond(nml,mhb,ipr)
|
---|
| 4204 | \shape default
|
---|
| 4205 | ):
|
---|
| 4206 | \newline
|
---|
| 4207 | This subroutine determines the number 'mhb' of the hydrogen bonds for
|
---|
| 4208 | the current conformation of the molecule and requires 'nml' as input -
|
---|
| 4209 | the index of the present molecule.
|
---|
| 4210 | The hydrogen bonds are printed out for '
|
---|
| 4211 | \begin_inset Formula $ipr>0$
|
---|
| 4212 | \end_inset
|
---|
| 4213 |
|
---|
| 4214 | '.
|
---|
| 4215 |
|
---|
| 4216 | \end_layout
|
---|
| 4217 |
|
---|
| 4218 | \begin_layout Subsubsection
|
---|
| 4219 | \begin_inset LatexCommand label
|
---|
| 4220 | name "ite:subroutine-HELIX"
|
---|
| 4221 |
|
---|
| 4222 | \end_inset
|
---|
| 4223 |
|
---|
| 4224 | subroutine HELIX
|
---|
| 4225 | \begin_inset LatexCommand index
|
---|
| 4226 | name "HELIX"
|
---|
| 4227 |
|
---|
| 4228 | \end_inset
|
---|
| 4229 |
|
---|
| 4230 |
|
---|
| 4231 | \end_layout
|
---|
| 4232 |
|
---|
| 4233 | \begin_layout Standard
|
---|
| 4234 | (Usage:
|
---|
| 4235 | \shape italic
|
---|
| 4236 | helix(nhel,mhel,nbet,mbet)
|
---|
| 4237 | \shape default
|
---|
| 4238 | ):
|
---|
| 4239 | \newline
|
---|
| 4240 | HELIX determines whether a residue is part of an
|
---|
| 4241 | \begin_inset Formula $\alpha$
|
---|
| 4242 | \end_inset
|
---|
| 4243 |
|
---|
| 4244 | -helix or
|
---|
| 4245 | \begin_inset Formula $\beta$
|
---|
| 4246 | \end_inset
|
---|
| 4247 |
|
---|
| 4248 | -sheet according to its backbone dihedral angles (
|
---|
| 4249 | \begin_inset Formula $\phi,\psi$
|
---|
| 4250 | \end_inset
|
---|
| 4251 |
|
---|
| 4252 | ) (ranges defined in a PARAMETER statement) and returnes the number of helical
|
---|
| 4253 | residues 'nhel', the number of helical segments 'mhel', and the corresponding
|
---|
| 4254 | quantities for
|
---|
| 4255 | \begin_inset Formula $\beta$
|
---|
| 4256 | \end_inset
|
---|
| 4257 |
|
---|
| 4258 | -strand elements 'nbet' and 'mbet'.
|
---|
| 4259 |
|
---|
| 4260 | \end_layout
|
---|
| 4261 |
|
---|
| 4262 | \begin_layout Subsubsection
|
---|
| 4263 | \begin_inset LatexCommand label
|
---|
| 4264 | name "ite:Subroutine-METROPOLIS"
|
---|
| 4265 |
|
---|
| 4266 | \end_inset
|
---|
| 4267 |
|
---|
| 4268 | Subroutine METROPOLIS
|
---|
| 4269 | \begin_inset LatexCommand index
|
---|
| 4270 | name "METROPOLIS"
|
---|
| 4271 |
|
---|
| 4272 | \end_inset
|
---|
| 4273 |
|
---|
| 4274 |
|
---|
| 4275 | \end_layout
|
---|
| 4276 |
|
---|
| 4277 | \begin_layout Standard
|
---|
| 4278 | (Usage:
|
---|
| 4279 | \shape italic
|
---|
| 4280 | call metropolis(eol,acz,weight)
|
---|
| 4281 | \shape default
|
---|
| 4282 | ):
|
---|
| 4283 | \newline
|
---|
| 4284 | The subroutine implements one Metropolis move for every dihedral angle
|
---|
| 4285 | and requires as input a weight function '
|
---|
| 4286 | \shape italic
|
---|
| 4287 | weight(eol)
|
---|
| 4288 | \shape default
|
---|
| 4289 | ' and the energy 'eol' of the present configuration.
|
---|
| 4290 | It returns in the variable 'eol' the energy of the configuration after
|
---|
| 4291 | 'nvr' (the number of non-fixed dihedral angles) updates.
|
---|
| 4292 | 'acz' accounts for the number of Metropolis moves were the proposed configurati
|
---|
| 4293 | on was accepted.
|
---|
| 4294 |
|
---|
| 4295 | \end_layout
|
---|
| 4296 |
|
---|
| 4297 | \begin_layout Subsubsection
|
---|
| 4298 | Subroutine OUTPDB
|
---|
| 4299 | \begin_inset LatexCommand index
|
---|
| 4300 | name "OUTPDB"
|
---|
| 4301 |
|
---|
| 4302 | \end_inset
|
---|
| 4303 |
|
---|
| 4304 |
|
---|
| 4305 | \end_layout
|
---|
| 4306 |
|
---|
| 4307 | \begin_layout Standard
|
---|
| 4308 | (Usage:
|
---|
| 4309 | \shape italic
|
---|
| 4310 | call outpdb(nml,pdbFileName)
|
---|
| 4311 | \shape default
|
---|
| 4312 | ):
|
---|
| 4313 | \newline
|
---|
| 4314 | The subroutine writes in the output file the coordinates of the atoms
|
---|
| 4315 | of given molecule.
|
---|
| 4316 | The format is compatible with the standard data representation format of
|
---|
| 4317 | the Brookhaven Protein Data bank.
|
---|
| 4318 | This subroutine requires as input the index 'nml' of the given molecule
|
---|
| 4319 | and the file name of the output-file.
|
---|
| 4320 | If nml=0, the configuration for all molecules in the system is written
|
---|
| 4321 | to a multi-model pdb file.
|
---|
| 4322 | \end_layout
|
---|
| 4323 |
|
---|
| 4324 | \begin_layout Subsubsection
|
---|
| 4325 | Subroutine OUTVAR
|
---|
| 4326 | \begin_inset LatexCommand index
|
---|
| 4327 | name "OUTVAR"
|
---|
| 4328 |
|
---|
| 4329 | \end_inset
|
---|
| 4330 |
|
---|
| 4331 |
|
---|
| 4332 | \end_layout
|
---|
| 4333 |
|
---|
| 4334 | \begin_layout Standard
|
---|
| 4335 | (Usage:
|
---|
| 4336 | \shape italic
|
---|
| 4337 | call outvar(nml, filename)
|
---|
| 4338 | \shape default
|
---|
| 4339 | ):
|
---|
| 4340 | \end_layout
|
---|
| 4341 |
|
---|
| 4342 | \begin_layout Standard
|
---|
| 4343 | This subroutine writes the dihedral angles of the current configuration
|
---|
| 4344 | of molecule '
|
---|
| 4345 | \shape italic
|
---|
| 4346 | nml
|
---|
| 4347 | \shape default
|
---|
| 4348 | ' to either standard output ('filename =
|
---|
| 4349 | \begin_inset Quotes eld
|
---|
| 4350 | \end_inset
|
---|
| 4351 |
|
---|
| 4352 |
|
---|
| 4353 | \begin_inset Quotes eld
|
---|
| 4354 | \end_inset
|
---|
| 4355 |
|
---|
| 4356 | ') or a dedicated file, where filename is the name of the file).
|
---|
| 4357 | The dihedral angles are written out in a form that allows to use them as
|
---|
| 4358 | configuration input file for SMMP.
|
---|
| 4359 | If nml=0, the configuration for all molecules in the system is printed.
|
---|
| 4360 |
|
---|
| 4361 | \end_layout
|
---|
| 4362 |
|
---|
| 4363 | \begin_layout Subsubsection
|
---|
| 4364 | Function grnd() and subroutine sgrnd(seed):
|
---|
| 4365 | \end_layout
|
---|
| 4366 |
|
---|
| 4367 | \begin_layout Standard
|
---|
| 4368 | Our package includes an implementation of the twister-mersenne random generator.
|
---|
| 4369 | Initialize the random number generator using
|
---|
| 4370 | \emph on
|
---|
| 4371 | call sgrnd(seed)
|
---|
| 4372 | \emph default
|
---|
| 4373 | , where
|
---|
| 4374 | \emph on
|
---|
| 4375 | seed
|
---|
| 4376 | \emph default
|
---|
| 4377 | is an integer.
|
---|
| 4378 | Each call off
|
---|
| 4379 | \emph on
|
---|
| 4380 | grnd()
|
---|
| 4381 | \emph default
|
---|
| 4382 | returns a new random number between 0 and 1 taken from a uniform distribution.
|
---|
| 4383 | \end_layout
|
---|
| 4384 |
|
---|
| 4385 | \begin_layout Subsubsection
|
---|
| 4386 | \begin_inset LatexCommand label
|
---|
| 4387 | name "ite:Subroutine-RGYR"
|
---|
| 4388 |
|
---|
| 4389 | \end_inset
|
---|
| 4390 |
|
---|
| 4391 | Subroutine RGYR
|
---|
| 4392 | \end_layout
|
---|
| 4393 |
|
---|
| 4394 | \begin_layout Standard
|
---|
| 4395 | (Usage:
|
---|
| 4396 | \shape italic
|
---|
| 4397 | call rgyr(nml,rgy,ee)
|
---|
| 4398 | \shape default
|
---|
| 4399 | ):
|
---|
| 4400 | \newline
|
---|
| 4401 | This subroutine calculates the radius-of-gyration 'rgy' and the end-to-end
|
---|
| 4402 | distance 'ee' for the protein molecule 'nml'.
|
---|
| 4403 | Both quantities characterize the compactness of a protein conformation.
|
---|
| 4404 |
|
---|
| 4405 | \end_layout
|
---|
| 4406 |
|
---|
| 4407 | \begin_layout Subsubsection
|
---|
| 4408 | Function RMSDFUN
|
---|
| 4409 | \begin_inset LatexCommand index
|
---|
| 4410 | name "RMSDFUN"
|
---|
| 4411 |
|
---|
| 4412 | \end_inset
|
---|
| 4413 |
|
---|
| 4414 |
|
---|
| 4415 | \end_layout
|
---|
| 4416 |
|
---|
| 4417 | \begin_layout Standard
|
---|
| 4418 | (Usage:
|
---|
| 4419 | \shape italic
|
---|
| 4420 | rmsd = rmsdfun(nml,ir1,ir2,ixat,xrf,yrf,zrf,isl)
|
---|
| 4421 | \shape default
|
---|
| 4422 | )
|
---|
| 4423 | \newline
|
---|
| 4424 | The real*8 function '
|
---|
| 4425 | \shape italic
|
---|
| 4426 | rmsdfun
|
---|
| 4427 | \shape default
|
---|
| 4428 | ' calculates the root-mean square-deviation (rmsd) between atom postions
|
---|
| 4429 | in the current configuration of molecule '
|
---|
| 4430 | \shape italic
|
---|
| 4431 | nml
|
---|
| 4432 | \shape default
|
---|
| 4433 | ' for a range of residues '
|
---|
| 4434 | \shape italic
|
---|
| 4435 | [ir1,ir2]
|
---|
| 4436 | \shape default
|
---|
| 4437 | ' and a reference structure given by arrays of atom coordinates '
|
---|
| 4438 | \shape italic
|
---|
| 4439 | xrf,yrf,zrf
|
---|
| 4440 | \shape default
|
---|
| 4441 | '.
|
---|
| 4442 | For each atom position in the current SMMP-structure the array '
|
---|
| 4443 | \shape italic
|
---|
| 4444 | ixat
|
---|
| 4445 | \shape default
|
---|
| 4446 | ' provides the index of the equivalent atom in the reference structure,
|
---|
| 4447 | or yields a value of '
|
---|
| 4448 | \shape italic
|
---|
| 4449 | 0
|
---|
| 4450 | \shape default
|
---|
| 4451 | ' if there is no equivalent.
|
---|
| 4452 | By setting '
|
---|
| 4453 | \shape italic
|
---|
| 4454 | isl=0
|
---|
| 4455 | \shape default
|
---|
| 4456 | ' the rmsd is calculated over all non-hydrogen (heavy) atoms, for '
|
---|
| 4457 | \shape italic
|
---|
| 4458 | isl = 1
|
---|
| 4459 | \shape default
|
---|
| 4460 | ' for backbone atoms only, and for '
|
---|
| 4461 | \shape italic
|
---|
| 4462 | isl = 2
|
---|
| 4463 | \shape default
|
---|
| 4464 | ' the rmsd is calculated only between C
|
---|
| 4465 | \begin_inset Formula $^{\alpha}$
|
---|
| 4466 | \end_inset
|
---|
| 4467 |
|
---|
| 4468 | -atoms.
|
---|
| 4469 | The routine '
|
---|
| 4470 | \shape italic
|
---|
| 4471 | rmsdfun
|
---|
| 4472 | \shape default
|
---|
| 4473 | ' may only be called
|
---|
| 4474 | \series bold
|
---|
| 4475 | after
|
---|
| 4476 | \series default
|
---|
| 4477 | an initial call of the subroutine '
|
---|
| 4478 | \shape italic
|
---|
| 4479 | rmsinit(nml,string)
|
---|
| 4480 | \shape default
|
---|
| 4481 | '.
|
---|
| 4482 | If
|
---|
| 4483 | \shape italic
|
---|
| 4484 | string = 'smmp'
|
---|
| 4485 | \shape default
|
---|
| 4486 | the reference configuration is a SMMP configuration, otherwise it is read
|
---|
| 4487 | in from a PDB-file which name given by '
|
---|
| 4488 | \shape italic
|
---|
| 4489 | string
|
---|
| 4490 | \shape default
|
---|
| 4491 | '.
|
---|
| 4492 |
|
---|
| 4493 | \end_layout
|
---|
| 4494 |
|
---|
| 4495 | \begin_layout Subsubsection
|
---|
| 4496 | Subroutine ZIMMER
|
---|
| 4497 | \begin_inset LatexCommand index
|
---|
| 4498 | name "ZIMMER"
|
---|
| 4499 |
|
---|
| 4500 | \end_inset
|
---|
| 4501 |
|
---|
| 4502 |
|
---|
| 4503 | \end_layout
|
---|
| 4504 |
|
---|
| 4505 | \begin_layout Standard
|
---|
| 4506 | (Usage:
|
---|
| 4507 | \shape italic
|
---|
| 4508 | call zimmer(nresi)
|
---|
| 4509 | \shape default
|
---|
| 4510 | ):
|
---|
| 4511 | \newline
|
---|
| 4512 | This subroutine analyzes the backbone dihedrals of a given conformation
|
---|
| 4513 | and characterizes the state of each pair of (
|
---|
| 4514 | \begin_inset Formula $\phi,\psi$
|
---|
| 4515 | \end_inset
|
---|
| 4516 |
|
---|
| 4517 | ) by its Zimmerman code.
|
---|
| 4518 | The subroutine requires as input the number of residues 'nresi' and returns
|
---|
| 4519 | the character string 'zimm' with the Zimmerman code of the present configuratio
|
---|
| 4520 | n (through a common block).
|
---|
| 4521 |
|
---|
| 4522 | \end_layout
|
---|
| 4523 |
|
---|
| 4524 | \begin_layout Section
|
---|
| 4525 | How to cite SMMP
|
---|
| 4526 | \end_layout
|
---|
| 4527 |
|
---|
| 4528 | \begin_layout Standard
|
---|
| 4529 | Use of SMMP should be acknowledged by quoting the following reference: F.
|
---|
| 4530 | Eisenmenger, U.H.E.
|
---|
| 4531 | Hansmann, Sh.
|
---|
| 4532 | Hayryan, C.-K.
|
---|
| 4533 | Hu,
|
---|
| 4534 | \series bold
|
---|
| 4535 | [SMMP] A Modern Package for Simulation of Proteins
|
---|
| 4536 | \series default
|
---|
| 4537 | ,
|
---|
| 4538 | \shape italic
|
---|
| 4539 | Comp.
|
---|
| 4540 | Phys.
|
---|
| 4541 | Comm.
|
---|
| 4542 |
|
---|
| 4543 | \shape default
|
---|
| 4544 |
|
---|
| 4545 | \series bold
|
---|
| 4546 | 138
|
---|
| 4547 | \series default
|
---|
| 4548 | (2001) 192-212;
|
---|
| 4549 | \newline
|
---|
| 4550 | F.
|
---|
| 4551 | Eisenmenger, U.H.E.
|
---|
| 4552 | Hansmann, Sh.
|
---|
| 4553 | Hayryan, C.-K.
|
---|
| 4554 | Hu,
|
---|
| 4555 | \series bold
|
---|
| 4556 | An Enhanced Version of SMMP - Open-Source Software Package for Simulation
|
---|
| 4557 | of Proteins
|
---|
| 4558 | \series default
|
---|
| 4559 | ,
|
---|
| 4560 | \shape italic
|
---|
| 4561 | Comp.Phys.
|
---|
| 4562 | Comm.
|
---|
| 4563 | 174 (2006) 422-
|
---|
| 4564 | \shape default
|
---|
| 4565 | 429;
|
---|
| 4566 | \newline
|
---|
| 4567 |
|
---|
| 4568 | \emph on
|
---|
| 4569 | J.
|
---|
| 4570 | H.
|
---|
| 4571 | Meinke, S.
|
---|
| 4572 | Mohanty, F.
|
---|
| 4573 | Eisenmenger and U.H.E.
|
---|
| 4574 | Hansmann,
|
---|
| 4575 | \series bold
|
---|
| 4576 | \emph default
|
---|
| 4577 | SMMP v.
|
---|
| 4578 | 3.0 --- Simulating proteins and protein interactions in Python and Fortran
|
---|
| 4579 | \series default
|
---|
| 4580 | , submitted to
|
---|
| 4581 | \emph on
|
---|
| 4582 | Comp.\InsetSpace ~
|
---|
| 4583 | Phys.\InsetSpace ~
|
---|
| 4584 | Comm.
|
---|
| 4585 | \newline
|
---|
| 4586 |
|
---|
| 4587 | \emph default
|
---|
| 4588 | Where appropriate, the program package's web-site should be quoted as:
|
---|
| 4589 | \series bold
|
---|
| 4590 | SMMP,
|
---|
| 4591 | \begin_inset LatexCommand url
|
---|
| 4592 | target "http://www.phy.mtu.edu/biophys/smmp.htm"
|
---|
| 4593 |
|
---|
| 4594 | \end_inset
|
---|
| 4595 |
|
---|
| 4596 | or
|
---|
| 4597 | \series default
|
---|
| 4598 |
|
---|
| 4599 | \begin_inset LatexCommand url
|
---|
| 4600 | target "http://www.smmp05.net"
|
---|
| 4601 |
|
---|
| 4602 | \end_inset
|
---|
| 4603 |
|
---|
| 4604 | .
|
---|
| 4605 |
|
---|
| 4606 | \end_layout
|
---|
| 4607 |
|
---|
| 4608 | \begin_layout Section
|
---|
| 4609 | Examples
|
---|
| 4610 | \begin_inset LatexCommand label
|
---|
| 4611 | name "sec:Examples"
|
---|
| 4612 |
|
---|
| 4613 | \end_inset
|
---|
| 4614 |
|
---|
| 4615 |
|
---|
| 4616 | \end_layout
|
---|
| 4617 |
|
---|
| 4618 | \begin_layout Standard
|
---|
| 4619 | All the examples can be found in the EXAMPLES subdirectory and should be
|
---|
| 4620 | run from there.
|
---|
| 4621 | All the serial examples can be built either from the top-level directory
|
---|
| 4622 | with
|
---|
| 4623 | \emph on
|
---|
| 4624 | make examples
|
---|
| 4625 | \emph default
|
---|
| 4626 | or from within the EXAMPLES directory with
|
---|
| 4627 | \emph on
|
---|
| 4628 | make
|
---|
| 4629 | \emph default
|
---|
| 4630 | .
|
---|
| 4631 | The MPI parallel tempering example is built from within the EXAMPLES directory
|
---|
| 4632 | with
|
---|
| 4633 | \emph on
|
---|
| 4634 | make parallel_tempering_p.
|
---|
| 4635 |
|
---|
| 4636 | \emph default
|
---|
| 4637 | The structure of all examples is very similar to Listing
|
---|
| 4638 | \begin_inset LatexCommand ref
|
---|
| 4639 | reference "listing:mainmc"
|
---|
| 4640 |
|
---|
| 4641 | \end_inset
|
---|
| 4642 |
|
---|
| 4643 | .
|
---|
| 4644 | We first initialize the force field we want to use, load the protein either
|
---|
| 4645 | from a sequence and a configuration file or from a PDB file, set the simulation
|
---|
| 4646 | parameters, and finally call the simulation subroutine.
|
---|
| 4647 | We use
|
---|
| 4648 | \shape italic
|
---|
| 4649 | \emph on
|
---|
| 4650 |
|
---|
| 4651 | \emph default
|
---|
| 4652 | grpn = 'nh2', grpc = 'cooh'
|
---|
| 4653 | \emph on
|
---|
| 4654 | as end groups in all of our examples.
|
---|
| 4655 | We also use a fixed value for the dielectric constant, so that
|
---|
| 4656 | \emph default
|
---|
| 4657 | epsd=.false.
|
---|
| 4658 |
|
---|
| 4659 | \emph on
|
---|
| 4660 | in all cases.
|
---|
| 4661 | \end_layout
|
---|
| 4662 |
|
---|
| 4663 | \begin_layout Standard
|
---|
| 4664 | The first example
|
---|
| 4665 | \begin_inset LatexCommand eqref
|
---|
| 4666 | reference "sub:Minimization-of-vacuum"
|
---|
| 4667 |
|
---|
| 4668 | \end_inset
|
---|
| 4669 |
|
---|
| 4670 | minimizes the energy of met-enkaphalin, a small endorphin with only 5 amino
|
---|
| 4671 | acids using a quasi-newton minimizer.
|
---|
| 4672 | The second examples
|
---|
| 4673 | \begin_inset LatexCommand eqref
|
---|
| 4674 | reference "sub:Structure-Determination-by"
|
---|
| 4675 |
|
---|
| 4676 | \end_inset
|
---|
| 4677 |
|
---|
| 4678 | tries to find the minimum vacuum energy structure of met-enkaphalin using
|
---|
| 4679 | simulated annealing.
|
---|
| 4680 | The third example
|
---|
| 4681 | \begin_inset LatexCommand eqref
|
---|
| 4682 | reference "sub:Calculation-of-Multicanonical"
|
---|
| 4683 |
|
---|
| 4684 | \end_inset
|
---|
| 4685 |
|
---|
| 4686 | shows how to calculate the estmated weights necessary for a multi-canonical
|
---|
| 4687 | Monte Carlo simulation.
|
---|
| 4688 | Met-enkaphalin again serves as sample system.
|
---|
| 4689 | In
|
---|
| 4690 | \begin_inset LatexCommand eqref
|
---|
| 4691 | reference "sub:Regularization-of-the"
|
---|
| 4692 |
|
---|
| 4693 | \end_inset
|
---|
| 4694 |
|
---|
| 4695 | we show how to regularize an experimental structure read from a PDB file.
|
---|
| 4696 | The force fields implemented use fixed bond lengths and valence angles.
|
---|
| 4697 | Without regularization, a structure read from a PDB file often has an unreasona
|
---|
| 4698 | bly high energy.
|
---|
| 4699 | Finally, we show how to perform parallel tempering simulations on multiple
|
---|
| 4700 | processors
|
---|
| 4701 | \begin_inset LatexCommand eqref
|
---|
| 4702 | reference "sub:Parallel-Tempering-simulation"
|
---|
| 4703 |
|
---|
| 4704 | \end_inset
|
---|
| 4705 |
|
---|
| 4706 | and on a single processor
|
---|
| 4707 | \begin_inset LatexCommand eqref
|
---|
| 4708 | reference "sub:Parallel-tempering-on"
|
---|
| 4709 |
|
---|
| 4710 | \end_inset
|
---|
| 4711 |
|
---|
| 4712 | .
|
---|
| 4713 | The sample output was generated on a system with two dual-core AMD Opteron
|
---|
| 4714 | 2216 processor running SUSE LINUX 10.1 (X86-64).
|
---|
| 4715 | The programs were compiled with Intels Fortran compiler with optimization
|
---|
| 4716 | set to -O2.
|
---|
| 4717 | \end_layout
|
---|
| 4718 |
|
---|
| 4719 | \begin_layout Subsection
|
---|
| 4720 | Minimization of vacuum energy from a given configuration
|
---|
| 4721 | \begin_inset LatexCommand label
|
---|
| 4722 | name "sub:Minimization-of-vacuum"
|
---|
| 4723 |
|
---|
| 4724 | \end_inset
|
---|
| 4725 |
|
---|
| 4726 |
|
---|
| 4727 | \end_layout
|
---|
| 4728 |
|
---|
| 4729 | \begin_layout Standard
|
---|
| 4730 | The MAIN module in minimization.f, has the following settings:
|
---|
| 4731 | \newline
|
---|
| 4732 |
|
---|
| 4733 | \shape italic
|
---|
| 4734 | \emph on
|
---|
| 4735 | ientyp = 0
|
---|
| 4736 | \newline
|
---|
| 4737 | sh2 = .false.
|
---|
| 4738 |
|
---|
| 4739 | \newline
|
---|
| 4740 | itysol = 0
|
---|
| 4741 | \newline
|
---|
| 4742 | iabin = 1
|
---|
| 4743 | \shape default
|
---|
| 4744 | ,
|
---|
| 4745 | \newline
|
---|
| 4746 |
|
---|
| 4747 | \emph default
|
---|
| 4748 |
|
---|
| 4749 | \newline
|
---|
| 4750 | which restrict energy calculations to evaluation of the ECEPP/3 energy
|
---|
| 4751 | (no protein-solvent interactions taken into account), choses
|
---|
| 4752 | \shape italic
|
---|
| 4753 | nh2
|
---|
| 4754 | \shape default
|
---|
| 4755 | as N-terminal group and at the C-terminus the
|
---|
| 4756 | \shape italic
|
---|
| 4757 | cooh
|
---|
| 4758 | \shape default
|
---|
| 4759 | -group, and the input is read from a sequence/configuration file.
|
---|
| 4760 | The simulation task subroutine is called with
|
---|
| 4761 | \newline
|
---|
| 4762 | imin = 1
|
---|
| 4763 | \newline
|
---|
| 4764 | maxit=10000
|
---|
| 4765 | \newline
|
---|
| 4766 | eps=1.0d-9
|
---|
| 4767 | \newline
|
---|
| 4768 |
|
---|
| 4769 | \shape italic
|
---|
| 4770 | call minim(imin,mait,eps)
|
---|
| 4771 | \shape default
|
---|
| 4772 | ,
|
---|
| 4773 | \newline
|
---|
| 4774 | i.e.
|
---|
| 4775 | the simulation task is the local minimization of the vacuum energy of a
|
---|
| 4776 | configuration using the Quasi-Newton algorithm.
|
---|
| 4777 | Compile the program with
|
---|
| 4778 | \emph on
|
---|
| 4779 | make minimization
|
---|
| 4780 | \emph default
|
---|
| 4781 | , SMMP with this default settings will minimize the configuration given
|
---|
| 4782 | in
|
---|
| 4783 | \shape italic
|
---|
| 4784 | enkefa.var
|
---|
| 4785 | \shape default
|
---|
| 4786 | .
|
---|
| 4787 | Running minimization from the EXAMPLES directory will lead to the following
|
---|
| 4788 | output:
|
---|
| 4789 | \begin_inset ERT
|
---|
| 4790 | status open
|
---|
| 4791 |
|
---|
| 4792 | \begin_layout Standard
|
---|
| 4793 |
|
---|
| 4794 |
|
---|
| 4795 | \backslash
|
---|
| 4796 | begin{verbatim}
|
---|
| 4797 | \end_layout
|
---|
| 4798 |
|
---|
| 4799 | \begin_layout Standard
|
---|
| 4800 |
|
---|
| 4801 | init_energy: itysol = 0
|
---|
| 4802 | \end_layout
|
---|
| 4803 |
|
---|
| 4804 | \begin_layout Standard
|
---|
| 4805 |
|
---|
| 4806 | init_energy: esol_scaling = F
|
---|
| 4807 | \end_layout
|
---|
| 4808 |
|
---|
| 4809 | \begin_layout Standard
|
---|
| 4810 |
|
---|
| 4811 | init_molecule: Solvent: 0
|
---|
| 4812 | \end_layout
|
---|
| 4813 |
|
---|
| 4814 | \begin_layout Standard
|
---|
| 4815 |
|
---|
| 4816 | File with sequence is enkefa.seq
|
---|
| 4817 | \end_layout
|
---|
| 4818 |
|
---|
| 4819 | \begin_layout Standard
|
---|
| 4820 |
|
---|
| 4821 | addend> Net charge of molecule # 1: 0.001
|
---|
| 4822 | \end_layout
|
---|
| 4823 |
|
---|
| 4824 | \begin_layout Standard
|
---|
| 4825 |
|
---|
| 4826 | \end_layout
|
---|
| 4827 |
|
---|
| 4828 | \begin_layout Standard
|
---|
| 4829 |
|
---|
| 4830 | enkefa.var
|
---|
| 4831 | \end_layout
|
---|
| 4832 |
|
---|
| 4833 | \begin_layout Standard
|
---|
| 4834 |
|
---|
| 4835 | \end_layout
|
---|
| 4836 |
|
---|
| 4837 | \begin_layout Standard
|
---|
| 4838 |
|
---|
| 4839 | redvar> Met-Enkephalin: residue 1 Tyr : x1 set -172.590
|
---|
| 4840 | \end_layout
|
---|
| 4841 |
|
---|
| 4842 | \begin_layout Standard
|
---|
| 4843 |
|
---|
| 4844 | redvar> Met-Enkephalin: residue 1 Tyr : x2 set 78.710
|
---|
| 4845 | \end_layout
|
---|
| 4846 |
|
---|
| 4847 | \begin_layout Standard
|
---|
| 4848 |
|
---|
| 4849 | redvar> Met-Enkephalin: residue 1 Tyr : x6 set -165.880
|
---|
| 4850 | \end_layout
|
---|
| 4851 |
|
---|
| 4852 | \begin_layout Standard
|
---|
| 4853 |
|
---|
| 4854 | redvar> Met-Enkephalin: residue 1 Tyr : phi set -86.240
|
---|
| 4855 | \end_layout
|
---|
| 4856 |
|
---|
| 4857 | \begin_layout Standard
|
---|
| 4858 |
|
---|
| 4859 | redvar> Met-Enkephalin: residue 2 Gly : psi set 156.180
|
---|
| 4860 | \end_layout
|
---|
| 4861 |
|
---|
| 4862 | \begin_layout Standard
|
---|
| 4863 |
|
---|
| 4864 | redvar> Met-Enkephalin: residue 2 Gly : omg set -180.000
|
---|
| 4865 | \end_layout
|
---|
| 4866 |
|
---|
| 4867 | \begin_layout Standard
|
---|
| 4868 |
|
---|
| 4869 | redvar> Met-Enkephalin: residue 2 Gly : phi set -154.530
|
---|
| 4870 | \end_layout
|
---|
| 4871 |
|
---|
| 4872 | \begin_layout Standard
|
---|
| 4873 |
|
---|
| 4874 | redvar> Met-Enkephalin: residue 3 Gly : psi set 83.640
|
---|
| 4875 | \end_layout
|
---|
| 4876 |
|
---|
| 4877 | \begin_layout Standard
|
---|
| 4878 |
|
---|
| 4879 | redvar> Met-Enkephalin: residue 3 Gly : omg set 180.000
|
---|
| 4880 | \end_layout
|
---|
| 4881 |
|
---|
| 4882 | \begin_layout Standard
|
---|
| 4883 |
|
---|
| 4884 | redvar> Met-Enkephalin: residue 3 Gly : phi set 83.660
|
---|
| 4885 | \end_layout
|
---|
| 4886 |
|
---|
| 4887 | \begin_layout Standard
|
---|
| 4888 |
|
---|
| 4889 | redvar> Met-Enkephalin: residue 4 Phe : psi set -73.860
|
---|
| 4890 | \end_layout
|
---|
| 4891 |
|
---|
| 4892 | \begin_layout Standard
|
---|
| 4893 |
|
---|
| 4894 | redvar> Met-Enkephalin: residue 4 Phe : omg set -180.000
|
---|
| 4895 | \end_layout
|
---|
| 4896 |
|
---|
| 4897 | \begin_layout Standard
|
---|
| 4898 |
|
---|
| 4899 | redvar> Met-Enkephalin: residue 4 Phe : x1 set 58.790
|
---|
| 4900 | \end_layout
|
---|
| 4901 |
|
---|
| 4902 | \begin_layout Standard
|
---|
| 4903 |
|
---|
| 4904 | redvar> Met-Enkephalin: residue 4 Phe : x2 set 94.600
|
---|
| 4905 | \end_layout
|
---|
| 4906 |
|
---|
| 4907 | \begin_layout Standard
|
---|
| 4908 |
|
---|
| 4909 | redvar> Met-Enkephalin: residue 4 Phe : phi set -137.040
|
---|
| 4910 | \end_layout
|
---|
| 4911 |
|
---|
| 4912 | \begin_layout Standard
|
---|
| 4913 |
|
---|
| 4914 | redvar> Met-Enkephalin: residue 5 Met : psi set 19.330
|
---|
| 4915 | \end_layout
|
---|
| 4916 |
|
---|
| 4917 | \begin_layout Standard
|
---|
| 4918 |
|
---|
| 4919 | redvar> Met-Enkephalin: residue 5 Met : omg set -180.000
|
---|
| 4920 | \end_layout
|
---|
| 4921 |
|
---|
| 4922 | \begin_layout Standard
|
---|
| 4923 |
|
---|
| 4924 | redvar> Met-Enkephalin: residue 5 Met : x1 set 52.760
|
---|
| 4925 | \end_layout
|
---|
| 4926 |
|
---|
| 4927 | \begin_layout Standard
|
---|
| 4928 |
|
---|
| 4929 | redvar> Met-Enkephalin: residue 5 Met : x2 set 175.280
|
---|
| 4930 | \end_layout
|
---|
| 4931 |
|
---|
| 4932 | \begin_layout Standard
|
---|
| 4933 |
|
---|
| 4934 | redvar> Met-Enkephalin: residue 5 Met : x3 set -179.830
|
---|
| 4935 | \end_layout
|
---|
| 4936 |
|
---|
| 4937 | \begin_layout Standard
|
---|
| 4938 |
|
---|
| 4939 | redvar> Met-Enkephalin: residue 5 Met : x4 set -58.570
|
---|
| 4940 | \end_layout
|
---|
| 4941 |
|
---|
| 4942 | \begin_layout Standard
|
---|
| 4943 |
|
---|
| 4944 | redvar> Met-Enkephalin: residue 5 Met : phi set -163.630
|
---|
| 4945 | \end_layout
|
---|
| 4946 |
|
---|
| 4947 | \begin_layout Standard
|
---|
| 4948 |
|
---|
| 4949 | redvar> Met-Enkephalin: residue 5 Met : pst set 160.450
|
---|
| 4950 | \end_layout
|
---|
| 4951 |
|
---|
| 4952 | \begin_layout Standard
|
---|
| 4953 |
|
---|
| 4954 | redvar> Met-Enkephalin: residue 5 Met : omt set 180.000
|
---|
| 4955 | \end_layout
|
---|
| 4956 |
|
---|
| 4957 | \begin_layout Standard
|
---|
| 4958 |
|
---|
| 4959 | \end_layout
|
---|
| 4960 |
|
---|
| 4961 | \begin_layout Standard
|
---|
| 4962 |
|
---|
| 4963 | \end_layout
|
---|
| 4964 |
|
---|
| 4965 | \begin_layout Standard
|
---|
| 4966 |
|
---|
| 4967 | Energy BEFORE minimization:
|
---|
| 4968 | \end_layout
|
---|
| 4969 |
|
---|
| 4970 | \begin_layout Standard
|
---|
| 4971 |
|
---|
| 4972 | \end_layout
|
---|
| 4973 |
|
---|
| 4974 | \begin_layout Standard
|
---|
| 4975 |
|
---|
| 4976 | Total: 0.10354E+04
|
---|
| 4977 | \end_layout
|
---|
| 4978 |
|
---|
| 4979 | \begin_layout Standard
|
---|
| 4980 |
|
---|
| 4981 | Coulomb: 0.1991E+02 Lennard-Jones: 0.1142E+03 HB: 0.9008E+03
|
---|
| 4982 | \end_layout
|
---|
| 4983 |
|
---|
| 4984 | \begin_layout Standard
|
---|
| 4985 |
|
---|
| 4986 | Variables: 0.4511E+00 Solvatation: 0.0000E+00
|
---|
| 4987 | \end_layout
|
---|
| 4988 |
|
---|
| 4989 | \begin_layout Standard
|
---|
| 4990 |
|
---|
| 4991 | \end_layout
|
---|
| 4992 |
|
---|
| 4993 | \begin_layout Standard
|
---|
| 4994 |
|
---|
| 4995 | Step 1: energy 0.489976E+05 ( 0.867243E+13 )
|
---|
| 4996 | \end_layout
|
---|
| 4997 |
|
---|
| 4998 | \begin_layout Standard
|
---|
| 4999 |
|
---|
| 5000 | Step 2: energy 0.108241E+03 ( 0.964364E+07 )
|
---|
| 5001 | \end_layout
|
---|
| 5002 |
|
---|
| 5003 | \begin_layout Standard
|
---|
| 5004 |
|
---|
| 5005 | Step 3: energy -0.632755E+00 ( 0.498256E+04 )
|
---|
| 5006 | \end_layout
|
---|
| 5007 |
|
---|
| 5008 | \begin_layout Standard
|
---|
| 5009 |
|
---|
| 5010 | Step 4: energy -0.739539E+01 ( 0.109979E+05 )
|
---|
| 5011 | \end_layout
|
---|
| 5012 |
|
---|
| 5013 | \begin_layout Standard
|
---|
| 5014 |
|
---|
| 5015 | Step 5: energy 0.517957E+03 ( 0.678892E+09 )
|
---|
| 5016 | \end_layout
|
---|
| 5017 |
|
---|
| 5018 | \begin_layout Standard
|
---|
| 5019 |
|
---|
| 5020 | Step 6: energy -0.767774E+01 ( 0.143880E+05 )
|
---|
| 5021 | \end_layout
|
---|
| 5022 |
|
---|
| 5023 | \begin_layout Standard
|
---|
| 5024 |
|
---|
| 5025 | Step 7: energy -0.818570E+01 ( 0.100364E+05 )
|
---|
| 5026 | \end_layout
|
---|
| 5027 |
|
---|
| 5028 | \begin_layout Standard
|
---|
| 5029 |
|
---|
| 5030 | Step 8: energy -0.938401E+01 ( 0.172508E+04 )
|
---|
| 5031 | \end_layout
|
---|
| 5032 |
|
---|
| 5033 | \begin_layout Standard
|
---|
| 5034 |
|
---|
| 5035 | Step 9: energy -0.109799E+02 ( 0.105718E+04 )
|
---|
| 5036 | \end_layout
|
---|
| 5037 |
|
---|
| 5038 | \begin_layout Standard
|
---|
| 5039 |
|
---|
| 5040 | Step 10: energy -0.116244E+02 ( 0.580821E+03 )
|
---|
| 5041 | \end_layout
|
---|
| 5042 |
|
---|
| 5043 | \begin_layout Standard
|
---|
| 5044 |
|
---|
| 5045 | Step 11: energy -0.116969E+02 ( 0.145676E+04 )
|
---|
| 5046 | \end_layout
|
---|
| 5047 |
|
---|
| 5048 | \begin_layout Standard
|
---|
| 5049 |
|
---|
| 5050 | Step 12: energy -0.118569E+02 ( 0.856882E+03 )
|
---|
| 5051 | \end_layout
|
---|
| 5052 |
|
---|
| 5053 | \begin_layout Standard
|
---|
| 5054 |
|
---|
| 5055 | Step 13: energy -0.119576E+02 ( 0.521381E+03 )
|
---|
| 5056 | \end_layout
|
---|
| 5057 |
|
---|
| 5058 | \begin_layout Standard
|
---|
| 5059 |
|
---|
| 5060 | Step 14: energy -0.120897E+02 ( 0.398602E+03 )
|
---|
| 5061 | \end_layout
|
---|
| 5062 |
|
---|
| 5063 | \begin_layout Standard
|
---|
| 5064 |
|
---|
| 5065 | Step 15: energy -0.121476E+02 ( 0.222201E+03 )
|
---|
| 5066 | \end_layout
|
---|
| 5067 |
|
---|
| 5068 | \begin_layout Standard
|
---|
| 5069 |
|
---|
| 5070 | ...
|
---|
| 5071 | \end_layout
|
---|
| 5072 |
|
---|
| 5073 | \begin_layout Standard
|
---|
| 5074 |
|
---|
| 5075 | ...
|
---|
| 5076 | \end_layout
|
---|
| 5077 |
|
---|
| 5078 | \begin_layout Standard
|
---|
| 5079 |
|
---|
| 5080 | ...
|
---|
| 5081 | \end_layout
|
---|
| 5082 |
|
---|
| 5083 | \begin_layout Standard
|
---|
| 5084 |
|
---|
| 5085 | Step 70: energy -0.124285E+02 ( 0.194869E-04 )
|
---|
| 5086 | \end_layout
|
---|
| 5087 |
|
---|
| 5088 | \begin_layout Standard
|
---|
| 5089 |
|
---|
| 5090 | Step 71: energy -0.124285E+02 ( 0.120524E-04 )
|
---|
| 5091 | \end_layout
|
---|
| 5092 |
|
---|
| 5093 | \begin_layout Standard
|
---|
| 5094 |
|
---|
| 5095 | Step 72: energy -0.124285E+02 ( 0.641640E-05 )
|
---|
| 5096 | \end_layout
|
---|
| 5097 |
|
---|
| 5098 | \begin_layout Standard
|
---|
| 5099 |
|
---|
| 5100 | Step 73: energy -0.124285E+02 ( 0.182141E-05 )
|
---|
| 5101 | \end_layout
|
---|
| 5102 |
|
---|
| 5103 | \begin_layout Standard
|
---|
| 5104 |
|
---|
| 5105 | Step 74: energy -0.124285E+02 ( 0.219308E-05 )
|
---|
| 5106 | \end_layout
|
---|
| 5107 |
|
---|
| 5108 | \begin_layout Standard
|
---|
| 5109 |
|
---|
| 5110 | Step 75: energy -0.124285E+02 ( 0.348349E-05 )
|
---|
| 5111 | \end_layout
|
---|
| 5112 |
|
---|
| 5113 | \begin_layout Standard
|
---|
| 5114 |
|
---|
| 5115 | Step 76: energy -0.124285E+02 ( 0.166901E-05 )
|
---|
| 5116 | \end_layout
|
---|
| 5117 |
|
---|
| 5118 | \begin_layout Standard
|
---|
| 5119 |
|
---|
| 5120 | Step 77: energy -0.124285E+02 ( 0.177102E-06 )
|
---|
| 5121 | \end_layout
|
---|
| 5122 |
|
---|
| 5123 | \begin_layout Standard
|
---|
| 5124 |
|
---|
| 5125 | Step 78: energy -0.124285E+02 ( 0.663522E-08 )
|
---|
| 5126 | \end_layout
|
---|
| 5127 |
|
---|
| 5128 | \begin_layout Standard
|
---|
| 5129 |
|
---|
| 5130 | Step 79: energy -0.124285E+02 ( 0.210693E-08 )
|
---|
| 5131 | \end_layout
|
---|
| 5132 |
|
---|
| 5133 | \begin_layout Standard
|
---|
| 5134 |
|
---|
| 5135 | Step 80: energy -0.124285E+02 ( 0.370905E-08 )
|
---|
| 5136 | \end_layout
|
---|
| 5137 |
|
---|
| 5138 | \begin_layout Standard
|
---|
| 5139 |
|
---|
| 5140 | Step 81: energy -0.124285E+02 ( 0.324300E-08 )
|
---|
| 5141 | \end_layout
|
---|
| 5142 |
|
---|
| 5143 | \begin_layout Standard
|
---|
| 5144 |
|
---|
| 5145 | Step 82: energy -0.124285E+02 ( 0.777363E-09 )
|
---|
| 5146 | \end_layout
|
---|
| 5147 |
|
---|
| 5148 | \begin_layout Standard
|
---|
| 5149 |
|
---|
| 5150 | Step 83: energy -0.124285E+02 ( 0.443358E-10 )
|
---|
| 5151 | \end_layout
|
---|
| 5152 |
|
---|
| 5153 | \begin_layout Standard
|
---|
| 5154 |
|
---|
| 5155 | Step 84: energy -0.124285E+02 ( 0.322695E-11 )
|
---|
| 5156 | \end_layout
|
---|
| 5157 |
|
---|
| 5158 | \begin_layout Standard
|
---|
| 5159 |
|
---|
| 5160 | Step 85: energy -0.124285E+02 ( 0.144369E-11 )
|
---|
| 5161 | \end_layout
|
---|
| 5162 |
|
---|
| 5163 | \begin_layout Standard
|
---|
| 5164 |
|
---|
| 5165 | Step 86: energy -0.124285E+02 ( 0.291517E-11 )
|
---|
| 5166 | \end_layout
|
---|
| 5167 |
|
---|
| 5168 | \begin_layout Standard
|
---|
| 5169 |
|
---|
| 5170 | Step 87: energy -0.124285E+02 ( 0.322695E-11 )
|
---|
| 5171 | \end_layout
|
---|
| 5172 |
|
---|
| 5173 | \begin_layout Standard
|
---|
| 5174 |
|
---|
| 5175 | ---- CONVERGENCE ----
|
---|
| 5176 | \end_layout
|
---|
| 5177 |
|
---|
| 5178 | \begin_layout Standard
|
---|
| 5179 |
|
---|
| 5180 | \end_layout
|
---|
| 5181 |
|
---|
| 5182 | \begin_layout Standard
|
---|
| 5183 |
|
---|
| 5184 | Final energies __________________________________________________
|
---|
| 5185 | \end_layout
|
---|
| 5186 |
|
---|
| 5187 | \begin_layout Standard
|
---|
| 5188 |
|
---|
| 5189 | Total: -0.12429E+02
|
---|
| 5190 | \end_layout
|
---|
| 5191 |
|
---|
| 5192 | \begin_layout Standard
|
---|
| 5193 |
|
---|
| 5194 | Coulomb: 0.2143E+02 Lennard-Jones: -0.2923E+02 HB: -0.6706E+01
|
---|
| 5195 | \end_layout
|
---|
| 5196 |
|
---|
| 5197 | \begin_layout Standard
|
---|
| 5198 |
|
---|
| 5199 | Variables: 0.2084E+01 Solvatation: 0.0000E+00
|
---|
| 5200 | \end_layout
|
---|
| 5201 |
|
---|
| 5202 | \begin_layout Standard
|
---|
| 5203 |
|
---|
| 5204 | \end_layout
|
---|
| 5205 |
|
---|
| 5206 | \begin_layout Standard
|
---|
| 5207 |
|
---|
| 5208 | Variables _________________
|
---|
| 5209 | \end_layout
|
---|
| 5210 |
|
---|
| 5211 | \begin_layout Standard
|
---|
| 5212 |
|
---|
| 5213 | \end_layout
|
---|
| 5214 |
|
---|
| 5215 | \begin_layout Standard
|
---|
| 5216 |
|
---|
| 5217 | x1 1 -173.2 ( 0.6)
|
---|
| 5218 | \end_layout
|
---|
| 5219 |
|
---|
| 5220 | \begin_layout Standard
|
---|
| 5221 |
|
---|
| 5222 | x2 1 79.3 ( 0.6)
|
---|
| 5223 | \end_layout
|
---|
| 5224 |
|
---|
| 5225 | \begin_layout Standard
|
---|
| 5226 |
|
---|
| 5227 | x6 1 -166.3 ( 0.5)
|
---|
| 5228 | \end_layout
|
---|
| 5229 |
|
---|
| 5230 | \begin_layout Standard
|
---|
| 5231 |
|
---|
| 5232 | phi 1 -83.1 ( 3.2)
|
---|
| 5233 | \end_layout
|
---|
| 5234 |
|
---|
| 5235 | \begin_layout Standard
|
---|
| 5236 |
|
---|
| 5237 | psi 2 155.8 ( 0.4)
|
---|
| 5238 | \end_layout
|
---|
| 5239 |
|
---|
| 5240 | \begin_layout Standard
|
---|
| 5241 |
|
---|
| 5242 | omg 2 -177.1 ( 2.9)
|
---|
| 5243 | \end_layout
|
---|
| 5244 |
|
---|
| 5245 | \begin_layout Standard
|
---|
| 5246 |
|
---|
| 5247 | phi 2 -154.2 ( 0.3)
|
---|
| 5248 | \end_layout
|
---|
| 5249 |
|
---|
| 5250 | \begin_layout Standard
|
---|
| 5251 |
|
---|
| 5252 | psi 3 85.8 ( 2.2)
|
---|
| 5253 | \end_layout
|
---|
| 5254 |
|
---|
| 5255 | \begin_layout Standard
|
---|
| 5256 |
|
---|
| 5257 | omg 3 168.5 ( 11.5)
|
---|
| 5258 | \end_layout
|
---|
| 5259 |
|
---|
| 5260 | \begin_layout Standard
|
---|
| 5261 |
|
---|
| 5262 | phi 3 83.0 ( 0.7)
|
---|
| 5263 | \end_layout
|
---|
| 5264 |
|
---|
| 5265 | \begin_layout Standard
|
---|
| 5266 |
|
---|
| 5267 | psi 4 -75.0 ( 1.2)
|
---|
| 5268 | \end_layout
|
---|
| 5269 |
|
---|
| 5270 | \begin_layout Standard
|
---|
| 5271 |
|
---|
| 5272 | omg 4 -170.0 ( 10.0)
|
---|
| 5273 | \end_layout
|
---|
| 5274 |
|
---|
| 5275 | \begin_layout Standard
|
---|
| 5276 |
|
---|
| 5277 | x1 4 58.9 ( 0.1)
|
---|
| 5278 | \end_layout
|
---|
| 5279 |
|
---|
| 5280 | \begin_layout Standard
|
---|
| 5281 |
|
---|
| 5282 | x2 4 94.5 ( 0.1)
|
---|
| 5283 | \end_layout
|
---|
| 5284 |
|
---|
| 5285 | \begin_layout Standard
|
---|
| 5286 |
|
---|
| 5287 | phi 4 -136.8 ( 0.2)
|
---|
| 5288 | \end_layout
|
---|
| 5289 |
|
---|
| 5290 | \begin_layout Standard
|
---|
| 5291 |
|
---|
| 5292 | psi 5 19.1 ( 0.2)
|
---|
| 5293 | \end_layout
|
---|
| 5294 |
|
---|
| 5295 | \begin_layout Standard
|
---|
| 5296 |
|
---|
| 5297 | omg 5 -174.1 ( 5.9)
|
---|
| 5298 | \end_layout
|
---|
| 5299 |
|
---|
| 5300 | \begin_layout Standard
|
---|
| 5301 |
|
---|
| 5302 | x1 5 52.9 ( 0.1)
|
---|
| 5303 | \end_layout
|
---|
| 5304 |
|
---|
| 5305 | \begin_layout Standard
|
---|
| 5306 |
|
---|
| 5307 | x2 5 175.3 ( 0.0)
|
---|
| 5308 | \end_layout
|
---|
| 5309 |
|
---|
| 5310 | \begin_layout Standard
|
---|
| 5311 |
|
---|
| 5312 | x3 5 -179.9 ( 0.0)
|
---|
| 5313 | \end_layout
|
---|
| 5314 |
|
---|
| 5315 | \begin_layout Standard
|
---|
| 5316 |
|
---|
| 5317 | x4 5 -58.6 ( 0.0)
|
---|
| 5318 | \end_layout
|
---|
| 5319 |
|
---|
| 5320 | \begin_layout Standard
|
---|
| 5321 |
|
---|
| 5322 | phi 5 -163.4 ( 0.2)
|
---|
| 5323 | \end_layout
|
---|
| 5324 |
|
---|
| 5325 | \begin_layout Standard
|
---|
| 5326 |
|
---|
| 5327 | pst 5 160.8 ( 0.3)
|
---|
| 5328 | \end_layout
|
---|
| 5329 |
|
---|
| 5330 | \begin_layout Standard
|
---|
| 5331 |
|
---|
| 5332 | omt 5 -179.8 ( 0.2)
|
---|
| 5333 | \end_layout
|
---|
| 5334 |
|
---|
| 5335 | \begin_layout Standard
|
---|
| 5336 |
|
---|
| 5337 | \end_layout
|
---|
| 5338 |
|
---|
| 5339 | \begin_layout Standard
|
---|
| 5340 |
|
---|
| 5341 | Gradient______________________________________________________________
|
---|
| 5342 |
|
---|
| 5343 | \end_layout
|
---|
| 5344 |
|
---|
| 5345 | \begin_layout Standard
|
---|
| 5346 |
|
---|
| 5347 | 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
|
---|
| 5348 | \end_layout
|
---|
| 5349 |
|
---|
| 5350 | \begin_layout Standard
|
---|
| 5351 |
|
---|
| 5352 | 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
|
---|
| 5353 | \end_layout
|
---|
| 5354 |
|
---|
| 5355 | \begin_layout Standard
|
---|
| 5356 |
|
---|
| 5357 | 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
|
---|
| 5358 | \end_layout
|
---|
| 5359 |
|
---|
| 5360 | \begin_layout Standard
|
---|
| 5361 |
|
---|
| 5362 |
|
---|
| 5363 | \backslash
|
---|
| 5364 | end{verbatim}
|
---|
| 5365 | \end_layout
|
---|
| 5366 |
|
---|
| 5367 | \end_inset
|
---|
| 5368 |
|
---|
| 5369 |
|
---|
| 5370 | \end_layout
|
---|
| 5371 |
|
---|
| 5372 | \begin_layout Subsection
|
---|
| 5373 | Structure Determination by Simulated Annealing
|
---|
| 5374 | \begin_inset LatexCommand label
|
---|
| 5375 | name "sub:Structure-Determination-by"
|
---|
| 5376 |
|
---|
| 5377 | \end_inset
|
---|
| 5378 |
|
---|
| 5379 |
|
---|
| 5380 | \end_layout
|
---|
| 5381 |
|
---|
| 5382 | \begin_layout Standard
|
---|
| 5383 | For the following simulated annealing run for Met-Enkephalin defined through
|
---|
| 5384 | its sequence file
|
---|
| 5385 | \shape italic
|
---|
| 5386 | enkefa.seq
|
---|
| 5387 | \shape default
|
---|
| 5388 | , another configuration file
|
---|
| 5389 | \shape italic
|
---|
| 5390 | enkefa.ann
|
---|
| 5391 | \shape default
|
---|
| 5392 | is used.
|
---|
| 5393 | In this configuration file the dihedral angles
|
---|
| 5394 | \shape italic
|
---|
| 5395 | omg
|
---|
| 5396 | \shape default
|
---|
| 5397 | and
|
---|
| 5398 | \shape italic
|
---|
| 5399 | omt
|
---|
| 5400 | \shape default
|
---|
| 5401 | are fixed at 180.0 degrees using
|
---|
| 5402 | \begin_inset ERT
|
---|
| 5403 | status open
|
---|
| 5404 |
|
---|
| 5405 | \begin_layout Standard
|
---|
| 5406 |
|
---|
| 5407 |
|
---|
| 5408 | \backslash
|
---|
| 5409 | begin{verbatim}
|
---|
| 5410 | \end_layout
|
---|
| 5411 |
|
---|
| 5412 | \begin_layout Standard
|
---|
| 5413 |
|
---|
| 5414 | om*: 180.0 &
|
---|
| 5415 | \end_layout
|
---|
| 5416 |
|
---|
| 5417 | \begin_layout Standard
|
---|
| 5418 |
|
---|
| 5419 |
|
---|
| 5420 | \backslash
|
---|
| 5421 | end{verbatim}
|
---|
| 5422 | \end_layout
|
---|
| 5423 |
|
---|
| 5424 | \end_inset
|
---|
| 5425 |
|
---|
| 5426 | .
|
---|
| 5427 | Simulated annealing performs only poorly when these angles are free to
|
---|
| 5428 | change.
|
---|
| 5429 | In this example we choose ECEPP/2 ( setting
|
---|
| 5430 | \shape italic
|
---|
| 5431 | sh2 = .true.
|
---|
| 5432 |
|
---|
| 5433 | \shape default
|
---|
| 5434 | and no protein-solvation interaction.
|
---|
| 5435 | Hence, we have the following settings for parameters in
|
---|
| 5436 | \shape italic
|
---|
| 5437 | annealing.f
|
---|
| 5438 | \shape default
|
---|
| 5439 | :
|
---|
| 5440 | \begin_inset ERT
|
---|
| 5441 | status open
|
---|
| 5442 |
|
---|
| 5443 | \begin_layout Standard
|
---|
| 5444 |
|
---|
| 5445 |
|
---|
| 5446 | \backslash
|
---|
| 5447 | begin{verbatim}
|
---|
| 5448 | \end_layout
|
---|
| 5449 |
|
---|
| 5450 | \begin_layout Standard
|
---|
| 5451 |
|
---|
| 5452 | ientyp = 0
|
---|
| 5453 | \end_layout
|
---|
| 5454 |
|
---|
| 5455 | \begin_layout Standard
|
---|
| 5456 |
|
---|
| 5457 | sh2 = .true.
|
---|
| 5458 |
|
---|
| 5459 | \end_layout
|
---|
| 5460 |
|
---|
| 5461 | \begin_layout Standard
|
---|
| 5462 |
|
---|
| 5463 | itysol = 0
|
---|
| 5464 | \end_layout
|
---|
| 5465 |
|
---|
| 5466 | \begin_layout Standard
|
---|
| 5467 |
|
---|
| 5468 | iabin = 1
|
---|
| 5469 | \end_layout
|
---|
| 5470 |
|
---|
| 5471 | \begin_layout Standard
|
---|
| 5472 |
|
---|
| 5473 |
|
---|
| 5474 | \backslash
|
---|
| 5475 | end{verbatim}
|
---|
| 5476 | \end_layout
|
---|
| 5477 |
|
---|
| 5478 | \end_inset
|
---|
| 5479 |
|
---|
| 5480 | .
|
---|
| 5481 | Our simulated annealing run consists of 100 Monte Carlo sweeps at the highest
|
---|
| 5482 | temperature (1000 K) followed by 100,000 sweeps during which the temperature
|
---|
| 5483 | is gradually decreased to a final temperature of 100 K.
|
---|
| 5484 | The progress of the simulation is monitored by writing data into the file
|
---|
| 5485 | `
|
---|
| 5486 | \shape italic
|
---|
| 5487 | time.d
|
---|
| 5488 | \shape default
|
---|
| 5489 | ' every 1000 sweeps.
|
---|
| 5490 | The simulation starts from a random configuration.
|
---|
| 5491 |
|
---|
| 5492 | \begin_inset ERT
|
---|
| 5493 | status open
|
---|
| 5494 |
|
---|
| 5495 | \begin_layout Standard
|
---|
| 5496 |
|
---|
| 5497 |
|
---|
| 5498 | \backslash
|
---|
| 5499 | begin{verbatim}
|
---|
| 5500 | \end_layout
|
---|
| 5501 |
|
---|
| 5502 | \begin_layout Standard
|
---|
| 5503 |
|
---|
| 5504 | lrand=.true.
|
---|
| 5505 |
|
---|
| 5506 | \end_layout
|
---|
| 5507 |
|
---|
| 5508 | \begin_layout Standard
|
---|
| 5509 |
|
---|
| 5510 | nequi=100,
|
---|
| 5511 | \end_layout
|
---|
| 5512 |
|
---|
| 5513 | \begin_layout Standard
|
---|
| 5514 |
|
---|
| 5515 | nswp=100000
|
---|
| 5516 | \end_layout
|
---|
| 5517 |
|
---|
| 5518 | \begin_layout Standard
|
---|
| 5519 |
|
---|
| 5520 | nmes=1000
|
---|
| 5521 | \end_layout
|
---|
| 5522 |
|
---|
| 5523 | \begin_layout Standard
|
---|
| 5524 |
|
---|
| 5525 | tmax=1000.0
|
---|
| 5526 | \end_layout
|
---|
| 5527 |
|
---|
| 5528 | \begin_layout Standard
|
---|
| 5529 |
|
---|
| 5530 | tmin=100.0
|
---|
| 5531 | \end_layout
|
---|
| 5532 |
|
---|
| 5533 | \begin_layout Standard
|
---|
| 5534 |
|
---|
| 5535 | \end_layout
|
---|
| 5536 |
|
---|
| 5537 | \begin_layout Standard
|
---|
| 5538 |
|
---|
| 5539 | call anneal(nequi, nsweeps, nmes, tmax, tmin, lrand)
|
---|
| 5540 | \end_layout
|
---|
| 5541 |
|
---|
| 5542 | \begin_layout Standard
|
---|
| 5543 |
|
---|
| 5544 |
|
---|
| 5545 | \backslash
|
---|
| 5546 | end{verbatim}
|
---|
| 5547 | \end_layout
|
---|
| 5548 |
|
---|
| 5549 | \end_inset
|
---|
| 5550 |
|
---|
| 5551 |
|
---|
| 5552 | \end_layout
|
---|
| 5553 |
|
---|
| 5554 | \begin_layout Standard
|
---|
| 5555 | After compiling the example with
|
---|
| 5556 | \emph on
|
---|
| 5557 | make annealing
|
---|
| 5558 | \emph default
|
---|
| 5559 | in the sub-directory
|
---|
| 5560 | \shape italic
|
---|
| 5561 | EXAMPLES,
|
---|
| 5562 | \shape default
|
---|
| 5563 |
|
---|
| 5564 | \shape italic
|
---|
| 5565 | \emph on
|
---|
| 5566 | we run the program by calling
|
---|
| 5567 | \shape default
|
---|
| 5568 | \emph default
|
---|
| 5569 |
|
---|
| 5570 | \shape italic
|
---|
| 5571 | annealing.
|
---|
| 5572 |
|
---|
| 5573 | \shape default
|
---|
| 5574 | The output will contain the energy of the start configuration, energy after
|
---|
| 5575 | equilibration, the average acceptance rate of moves in the simulated annealing
|
---|
| 5576 | run, the final configuration (and its energy) and the configuration with
|
---|
| 5577 | the lowest energy found in this run:
|
---|
| 5578 | \begin_inset ERT
|
---|
| 5579 | status open
|
---|
| 5580 |
|
---|
| 5581 | \begin_layout Standard
|
---|
| 5582 |
|
---|
| 5583 |
|
---|
| 5584 | \backslash
|
---|
| 5585 | begin{verbatim}
|
---|
| 5586 | \end_layout
|
---|
| 5587 |
|
---|
| 5588 | \begin_layout Standard
|
---|
| 5589 |
|
---|
| 5590 | init_energy: itysol = 0
|
---|
| 5591 | \end_layout
|
---|
| 5592 |
|
---|
| 5593 | \begin_layout Standard
|
---|
| 5594 |
|
---|
| 5595 | init_energy: esol_scaling = F
|
---|
| 5596 | \end_layout
|
---|
| 5597 |
|
---|
| 5598 | \begin_layout Standard
|
---|
| 5599 |
|
---|
| 5600 | init_molecule: Solvent: 0
|
---|
| 5601 | \end_layout
|
---|
| 5602 |
|
---|
| 5603 | \begin_layout Standard
|
---|
| 5604 |
|
---|
| 5605 | File with SEQUENCE: enkefa.seq
|
---|
| 5606 | \end_layout
|
---|
| 5607 |
|
---|
| 5608 | \begin_layout Standard
|
---|
| 5609 |
|
---|
| 5610 | enkefa.ann
|
---|
| 5611 | \end_layout
|
---|
| 5612 |
|
---|
| 5613 | \begin_layout Standard
|
---|
| 5614 |
|
---|
| 5615 | \end_layout
|
---|
| 5616 |
|
---|
| 5617 | \begin_layout Standard
|
---|
| 5618 |
|
---|
| 5619 | redvar> Met-Enkephalin: residue 2 Gly : omg set 180.000 Fixed
|
---|
| 5620 | \end_layout
|
---|
| 5621 |
|
---|
| 5622 | \begin_layout Standard
|
---|
| 5623 |
|
---|
| 5624 | redvar> Met-Enkephalin: residue 3 Gly : omg set 180.000 Fixed
|
---|
| 5625 | \end_layout
|
---|
| 5626 |
|
---|
| 5627 | \begin_layout Standard
|
---|
| 5628 |
|
---|
| 5629 | redvar> Met-Enkephalin: residue 4 Phe : omg set 180.000 Fixed
|
---|
| 5630 | \end_layout
|
---|
| 5631 |
|
---|
| 5632 | \begin_layout Standard
|
---|
| 5633 |
|
---|
| 5634 | redvar> Met-Enkephalin: residue 5 Met : omg set 180.000 Fixed
|
---|
| 5635 | \end_layout
|
---|
| 5636 |
|
---|
| 5637 | \begin_layout Standard
|
---|
| 5638 |
|
---|
| 5639 | redvar> Met-Enkephalin: residue 5 Met : omt set 180.000 Fixed
|
---|
| 5640 | \end_layout
|
---|
| 5641 |
|
---|
| 5642 | \begin_layout Standard
|
---|
| 5643 |
|
---|
| 5644 | redvar> Molecule Met-Enkephalin: 19 variable(s) remain unchanged
|
---|
| 5645 | \end_layout
|
---|
| 5646 |
|
---|
| 5647 | \begin_layout Standard
|
---|
| 5648 |
|
---|
| 5649 | \end_layout
|
---|
| 5650 |
|
---|
| 5651 | \begin_layout Standard
|
---|
| 5652 |
|
---|
| 5653 | energy of start configuration: 0.75921E+09
|
---|
| 5654 | \end_layout
|
---|
| 5655 |
|
---|
| 5656 | \begin_layout Standard
|
---|
| 5657 |
|
---|
| 5658 | \end_layout
|
---|
| 5659 |
|
---|
| 5660 | \begin_layout Standard
|
---|
| 5661 |
|
---|
| 5662 | Energy after equilibration: 11.0835755006373
|
---|
| 5663 | \end_layout
|
---|
| 5664 |
|
---|
| 5665 | \begin_layout Standard
|
---|
| 5666 |
|
---|
| 5667 | acceptance rate: 0.181430817270775
|
---|
| 5668 | \end_layout
|
---|
| 5669 |
|
---|
| 5670 | \begin_layout Standard
|
---|
| 5671 |
|
---|
| 5672 | \end_layout
|
---|
| 5673 |
|
---|
| 5674 | \begin_layout Standard
|
---|
| 5675 |
|
---|
| 5676 | last energy -8.03108763810183
|
---|
| 5677 | \end_layout
|
---|
| 5678 |
|
---|
| 5679 | \begin_layout Standard
|
---|
| 5680 |
|
---|
| 5681 | 1 : 1 : x1 : -168.428
|
---|
| 5682 | \end_layout
|
---|
| 5683 |
|
---|
| 5684 | \begin_layout Standard
|
---|
| 5685 |
|
---|
| 5686 | 1 : 1 : x2 : 89.562
|
---|
| 5687 | \end_layout
|
---|
| 5688 |
|
---|
| 5689 | \begin_layout Standard
|
---|
| 5690 |
|
---|
| 5691 | 1 : 1 : x6 : -2.861
|
---|
| 5692 | \end_layout
|
---|
| 5693 |
|
---|
| 5694 | \begin_layout Standard
|
---|
| 5695 |
|
---|
| 5696 | 1 : 1 : phi : -112.654
|
---|
| 5697 | \end_layout
|
---|
| 5698 |
|
---|
| 5699 | \begin_layout Standard
|
---|
| 5700 |
|
---|
| 5701 | 1 : 2 : psi : 156.420
|
---|
| 5702 | \end_layout
|
---|
| 5703 |
|
---|
| 5704 | \begin_layout Standard
|
---|
| 5705 |
|
---|
| 5706 | 1 : 2 : omg : -180.000 &
|
---|
| 5707 | \end_layout
|
---|
| 5708 |
|
---|
| 5709 | \begin_layout Standard
|
---|
| 5710 |
|
---|
| 5711 | 1 : 2 : phi : -174.567
|
---|
| 5712 | \end_layout
|
---|
| 5713 |
|
---|
| 5714 | \begin_layout Standard
|
---|
| 5715 |
|
---|
| 5716 | 1 : 3 : psi : 146.718
|
---|
| 5717 | \end_layout
|
---|
| 5718 |
|
---|
| 5719 | \begin_layout Standard
|
---|
| 5720 |
|
---|
| 5721 | 1 : 3 : omg : -180.000 &
|
---|
| 5722 | \end_layout
|
---|
| 5723 |
|
---|
| 5724 | \begin_layout Standard
|
---|
| 5725 |
|
---|
| 5726 | 1 : 3 : phi : 68.148
|
---|
| 5727 | \end_layout
|
---|
| 5728 |
|
---|
| 5729 | \begin_layout Standard
|
---|
| 5730 |
|
---|
| 5731 | 1 : 4 : psi : -96.563
|
---|
| 5732 | \end_layout
|
---|
| 5733 |
|
---|
| 5734 | \begin_layout Standard
|
---|
| 5735 |
|
---|
| 5736 | 1 : 4 : omg : -180.000 &
|
---|
| 5737 | \end_layout
|
---|
| 5738 |
|
---|
| 5739 | \begin_layout Standard
|
---|
| 5740 |
|
---|
| 5741 | 1 : 4 : x1 : 59.864
|
---|
| 5742 | \end_layout
|
---|
| 5743 |
|
---|
| 5744 | \begin_layout Standard
|
---|
| 5745 |
|
---|
| 5746 | 1 : 4 : x2 : -83.907
|
---|
| 5747 | \end_layout
|
---|
| 5748 |
|
---|
| 5749 | \begin_layout Standard
|
---|
| 5750 |
|
---|
| 5751 | 1 : 4 : phi : -141.914
|
---|
| 5752 | \end_layout
|
---|
| 5753 |
|
---|
| 5754 | \begin_layout Standard
|
---|
| 5755 |
|
---|
| 5756 | 1 : 5 : psi : 20.747
|
---|
| 5757 | \end_layout
|
---|
| 5758 |
|
---|
| 5759 | \begin_layout Standard
|
---|
| 5760 |
|
---|
| 5761 | 1 : 5 : omg : -180.000 &
|
---|
| 5762 | \end_layout
|
---|
| 5763 |
|
---|
| 5764 | \begin_layout Standard
|
---|
| 5765 |
|
---|
| 5766 | 1 : 5 : x1 : 61.133
|
---|
| 5767 | \end_layout
|
---|
| 5768 |
|
---|
| 5769 | \begin_layout Standard
|
---|
| 5770 |
|
---|
| 5771 | 1 : 5 : x2 : -174.118
|
---|
| 5772 | \end_layout
|
---|
| 5773 |
|
---|
| 5774 | \begin_layout Standard
|
---|
| 5775 |
|
---|
| 5776 | 1 : 5 : x3 : 176.917
|
---|
| 5777 | \end_layout
|
---|
| 5778 |
|
---|
| 5779 | \begin_layout Standard
|
---|
| 5780 |
|
---|
| 5781 | 1 : 5 : x4 : -178.096
|
---|
| 5782 | \end_layout
|
---|
| 5783 |
|
---|
| 5784 | \begin_layout Standard
|
---|
| 5785 |
|
---|
| 5786 | 1 : 5 : phi : -162.246
|
---|
| 5787 | \end_layout
|
---|
| 5788 |
|
---|
| 5789 | \begin_layout Standard
|
---|
| 5790 |
|
---|
| 5791 | 1 : 5 : pst : 161.616
|
---|
| 5792 | \end_layout
|
---|
| 5793 |
|
---|
| 5794 | \begin_layout Standard
|
---|
| 5795 |
|
---|
| 5796 | 1 : 5 : omt : -180.000 &
|
---|
| 5797 | \end_layout
|
---|
| 5798 |
|
---|
| 5799 | \begin_layout Standard
|
---|
| 5800 |
|
---|
| 5801 | \end_layout
|
---|
| 5802 |
|
---|
| 5803 | \begin_layout Standard
|
---|
| 5804 |
|
---|
| 5805 | lowest energy ever found: 63297 -9.40635361798398
|
---|
| 5806 | \end_layout
|
---|
| 5807 |
|
---|
| 5808 | \begin_layout Standard
|
---|
| 5809 |
|
---|
| 5810 |
|
---|
| 5811 | \backslash
|
---|
| 5812 | end{verbatim}
|
---|
| 5813 | \end_layout
|
---|
| 5814 |
|
---|
| 5815 | \end_inset
|
---|
| 5816 |
|
---|
| 5817 | The random start configuration, final configuration and lowest-energy configura
|
---|
| 5818 | tion are also written in PDB-format into the files
|
---|
| 5819 | \shape italic
|
---|
| 5820 | start.pdb
|
---|
| 5821 | \shape default
|
---|
| 5822 | ,
|
---|
| 5823 | \shape italic
|
---|
| 5824 | final.pdb
|
---|
| 5825 | \shape default
|
---|
| 5826 | and
|
---|
| 5827 | \shape italic
|
---|
| 5828 | global.pdb
|
---|
| 5829 | \shape default
|
---|
| 5830 | allowing for easy visualization of these configurations with programs graphical
|
---|
| 5831 | ly displaying PDB-structures.
|
---|
| 5832 | The progress of the simulated annealing run is monitored through the time
|
---|
| 5833 | series in file
|
---|
| 5834 | \shape italic
|
---|
| 5835 | time.d
|
---|
| 5836 | \shape default
|
---|
| 5837 | which list the Monte Carlo sweep, temperature, ECEPP/2 energy, radius-of-gyrati
|
---|
| 5838 | on, the partial energy terms
|
---|
| 5839 | \begin_inset Formula $E_{\mbox{hb}}$
|
---|
| 5840 | \end_inset
|
---|
| 5841 |
|
---|
| 5842 | ,
|
---|
| 5843 | \begin_inset Formula $E_{\mbox{vdW}}$
|
---|
| 5844 | \end_inset
|
---|
| 5845 |
|
---|
| 5846 | ,
|
---|
| 5847 | \begin_inset Formula $E_{\mbox{C}}$
|
---|
| 5848 | \end_inset
|
---|
| 5849 |
|
---|
| 5850 | ,
|
---|
| 5851 | \begin_inset Formula $E_{\mbox{vr}}$
|
---|
| 5852 | \end_inset
|
---|
| 5853 |
|
---|
| 5854 | and the Zimmerman-coding of the present configuration.
|
---|
| 5855 | All the terms related to the solvent have been replaced by a single dot
|
---|
| 5856 | per column in the sample below.
|
---|
| 5857 |
|
---|
| 5858 | \begin_inset ERT
|
---|
| 5859 | status open
|
---|
| 5860 |
|
---|
| 5861 | \begin_layout Standard
|
---|
| 5862 |
|
---|
| 5863 |
|
---|
| 5864 | \backslash
|
---|
| 5865 | begin{verbatim}
|
---|
| 5866 | \end_layout
|
---|
| 5867 |
|
---|
| 5868 | \begin_layout Standard
|
---|
| 5869 |
|
---|
| 5870 | # $Id: anneal.f 192 2007-01-02 14:06:25Z meinke $
|
---|
| 5871 | \end_layout
|
---|
| 5872 |
|
---|
| 5873 | \begin_layout Standard
|
---|
| 5874 |
|
---|
| 5875 | # nsw, temp, eol, eysl, eyslh, eyslp, asa, rgy,
|
---|
| 5876 | \end_layout
|
---|
| 5877 |
|
---|
| 5878 | \begin_layout Standard
|
---|
| 5879 |
|
---|
| 5880 | # rgyh, rgyp, eyhb, eyvw, eyel, eyvr, zimm
|
---|
| 5881 | \end_layout
|
---|
| 5882 |
|
---|
| 5883 | \begin_layout Standard
|
---|
| 5884 |
|
---|
| 5885 | 0 1000.000 8.045 ....
|
---|
| 5886 | 4.542 ..
|
---|
| 5887 | -3.992 -14.929 23.308 3.658 ghcBD
|
---|
| 5888 | \end_layout
|
---|
| 5889 |
|
---|
| 5890 | \begin_layout Standard
|
---|
| 5891 |
|
---|
| 5892 | 1000 977.237 16.397 ....
|
---|
| 5893 | 5.835 ..
|
---|
| 5894 | -2.029 -11.821 24.061 6.186 BDeCG
|
---|
| 5895 | \end_layout
|
---|
| 5896 |
|
---|
| 5897 | \begin_layout Standard
|
---|
| 5898 |
|
---|
| 5899 | 2000 954.993 16.147 ....
|
---|
| 5900 | 5.302 ..
|
---|
| 5901 | -1.786 -11.072 25.230 3.775 AdEDA
|
---|
| 5902 | \end_layout
|
---|
| 5903 |
|
---|
| 5904 | \begin_layout Standard
|
---|
| 5905 |
|
---|
| 5906 | 3000 933.254 26.320 ....
|
---|
| 5907 | 6.434 ..
|
---|
| 5908 | -1.324 -4.642 25.514 6.771 EecFC
|
---|
| 5909 | \end_layout
|
---|
| 5910 |
|
---|
| 5911 | \begin_layout Standard
|
---|
| 5912 |
|
---|
| 5913 | 4000 912.011 14.884 ....
|
---|
| 5914 | 5.145 ..
|
---|
| 5915 | -2.474 -13.559 25.449 5.469 EHDDB
|
---|
| 5916 | \end_layout
|
---|
| 5917 |
|
---|
| 5918 | \begin_layout Standard
|
---|
| 5919 |
|
---|
| 5920 | 5000 891.251 21.650 ....
|
---|
| 5921 | 5.882 ..
|
---|
| 5922 | -1.179 -8.380 27.125 4.083 EHfEB
|
---|
| 5923 | \end_layout
|
---|
| 5924 |
|
---|
| 5925 | \begin_layout Standard
|
---|
| 5926 |
|
---|
| 5927 | 6000 870.964 13.854 ....
|
---|
| 5928 | 5.806 ..
|
---|
| 5929 | -2.271 -12.703 25.621 3.207 EcaEh
|
---|
| 5930 | \end_layout
|
---|
| 5931 |
|
---|
| 5932 | \begin_layout Standard
|
---|
| 5933 |
|
---|
| 5934 | 7000 851.138 19.786 ....
|
---|
| 5935 | 5.439 ..
|
---|
| 5936 | -1.952 -9.254 26.428 4.565 EHaAE
|
---|
| 5937 | \end_layout
|
---|
| 5938 |
|
---|
| 5939 | \begin_layout Standard
|
---|
| 5940 |
|
---|
| 5941 | 8000 831.764 14.299 ....
|
---|
| 5942 | 5.986 ..
|
---|
| 5943 | -1.596 -16.538 24.699 7.735 EECEF
|
---|
| 5944 | \end_layout
|
---|
| 5945 |
|
---|
| 5946 | \begin_layout Standard
|
---|
| 5947 |
|
---|
| 5948 | 9000 812.831 7.773 ....
|
---|
| 5949 | 4.915 ..
|
---|
| 5950 | -2.819 -16.392 24.850 2.134 EECBB
|
---|
| 5951 | \end_layout
|
---|
| 5952 |
|
---|
| 5953 | \begin_layout Standard
|
---|
| 5954 |
|
---|
| 5955 | ...
|
---|
| 5956 | \end_layout
|
---|
| 5957 |
|
---|
| 5958 | \begin_layout Standard
|
---|
| 5959 |
|
---|
| 5960 | ...
|
---|
| 5961 | \end_layout
|
---|
| 5962 |
|
---|
| 5963 | \begin_layout Standard
|
---|
| 5964 |
|
---|
| 5965 | ...
|
---|
| 5966 | \end_layout
|
---|
| 5967 |
|
---|
| 5968 | \begin_layout Standard
|
---|
| 5969 |
|
---|
| 5970 | 91000 123.027 -8.381 ....
|
---|
| 5971 | 4.414 ..
|
---|
| 5972 | -5.162 -26.932 22.230 1.483 FEcDE
|
---|
| 5973 | \end_layout
|
---|
| 5974 |
|
---|
| 5975 | \begin_layout Standard
|
---|
| 5976 |
|
---|
| 5977 | 92000 120.226 -6.302 ....
|
---|
| 5978 | 4.439 ..
|
---|
| 5979 | -4.825 -25.727 22.824 1.426 EEcDE
|
---|
| 5980 | \end_layout
|
---|
| 5981 |
|
---|
| 5982 | \begin_layout Standard
|
---|
| 5983 |
|
---|
| 5984 | 93000 117.490 -6.655 ....
|
---|
| 5985 | 4.413 ..
|
---|
| 5986 | -4.355 -25.081 21.937 0.845 FEcDE
|
---|
| 5987 | \end_layout
|
---|
| 5988 |
|
---|
| 5989 | \begin_layout Standard
|
---|
| 5990 |
|
---|
| 5991 | 94000 114.815 -8.190 ....
|
---|
| 5992 | 4.523 ..
|
---|
| 5993 | -6.848 -24.025 21.598 1.086 FEcDE
|
---|
| 5994 | \end_layout
|
---|
| 5995 |
|
---|
| 5996 | \begin_layout Standard
|
---|
| 5997 |
|
---|
| 5998 | 95000 112.202 -5.965 ....
|
---|
| 5999 | 4.434 ..
|
---|
| 6000 | -5.052 -24.021 21.995 1.114 EEcDE
|
---|
| 6001 | \end_layout
|
---|
| 6002 |
|
---|
| 6003 | \begin_layout Standard
|
---|
| 6004 |
|
---|
| 6005 | 96000 109.648 -7.081 ....
|
---|
| 6006 | 4.444 ..
|
---|
| 6007 | -4.717 -25.137 22.669 0.104 EEcDE
|
---|
| 6008 | \end_layout
|
---|
| 6009 |
|
---|
| 6010 | \begin_layout Standard
|
---|
| 6011 |
|
---|
| 6012 | 97000 107.152 -8.042 ....
|
---|
| 6013 | 4.561 ..
|
---|
| 6014 | -4.969 -25.544 21.850 0.621 FEcDE
|
---|
| 6015 | \end_layout
|
---|
| 6016 |
|
---|
| 6017 | \begin_layout Standard
|
---|
| 6018 |
|
---|
| 6019 | 98000 104.713 -7.342 ....
|
---|
| 6020 | 4.439 ..
|
---|
| 6021 | -4.737 -26.152 22.463 1.083 FEcDE
|
---|
| 6022 | \end_layout
|
---|
| 6023 |
|
---|
| 6024 | \begin_layout Standard
|
---|
| 6025 |
|
---|
| 6026 | 99000 102.329 -6.561 ....
|
---|
| 6027 | 4.438 ..
|
---|
| 6028 | -3.975 -25.213 21.963 0.664 FEcDE
|
---|
| 6029 | \end_layout
|
---|
| 6030 |
|
---|
| 6031 | \begin_layout Standard
|
---|
| 6032 |
|
---|
| 6033 | 100000 100.000 -8.031 ....
|
---|
| 6034 | 4.433 ..
|
---|
| 6035 | -5.231 -25.792 22.659 0.333 EEcDE
|
---|
| 6036 | \end_layout
|
---|
| 6037 |
|
---|
| 6038 | \begin_layout Standard
|
---|
| 6039 |
|
---|
| 6040 |
|
---|
| 6041 | \backslash
|
---|
| 6042 | end{verbatim}
|
---|
| 6043 | \end_layout
|
---|
| 6044 |
|
---|
| 6045 | \end_inset
|
---|
| 6046 |
|
---|
| 6047 |
|
---|
| 6048 | \end_layout
|
---|
| 6049 |
|
---|
| 6050 | \begin_layout Subsection
|
---|
| 6051 | Calculation of Multicanonical Parameters
|
---|
| 6052 | \begin_inset LatexCommand label
|
---|
| 6053 | name "sub:Calculation-of-Multicanonical"
|
---|
| 6054 |
|
---|
| 6055 | \end_inset
|
---|
| 6056 |
|
---|
| 6057 |
|
---|
| 6058 | \end_layout
|
---|
| 6059 |
|
---|
| 6060 | \begin_layout Standard
|
---|
| 6061 | In the following example, multicanonical parameters are calculated for met-enkep
|
---|
| 6062 | halin (with fixed omega angles) in gas-phase simulations relying on the
|
---|
| 6063 | ECEPP/3 force-field.
|
---|
| 6064 |
|
---|
| 6065 | \shape italic
|
---|
| 6066 | \emph on
|
---|
| 6067 | The functions
|
---|
| 6068 | \shape default
|
---|
| 6069 | \emph default
|
---|
| 6070 |
|
---|
| 6071 | \shape italic
|
---|
| 6072 | mulcan_par
|
---|
| 6073 | \shape default
|
---|
| 6074 |
|
---|
| 6075 | \shape italic
|
---|
| 6076 | \emph on
|
---|
| 6077 | and
|
---|
| 6078 | \shape default
|
---|
| 6079 | \emph default
|
---|
| 6080 |
|
---|
| 6081 | \shape italic
|
---|
| 6082 | mulcan_sim
|
---|
| 6083 | \shape default
|
---|
| 6084 | are part of the module
|
---|
| 6085 | \emph on
|
---|
| 6086 | multicanonical.
|
---|
| 6087 |
|
---|
| 6088 | \emph default
|
---|
| 6089 | To use the module, include
|
---|
| 6090 | \emph on
|
---|
| 6091 | use multicanonical
|
---|
| 6092 | \emph default
|
---|
| 6093 | in
|
---|
| 6094 | \emph on
|
---|
| 6095 | main
|
---|
| 6096 | \emph default
|
---|
| 6097 | .
|
---|
| 6098 | For this example, we set the following parameters in '
|
---|
| 6099 | \shape italic
|
---|
| 6100 | main
|
---|
| 6101 | \shape default
|
---|
| 6102 | ':
|
---|
| 6103 | \end_layout
|
---|
| 6104 |
|
---|
| 6105 | \begin_layout Standard
|
---|
| 6106 | \begin_inset ERT
|
---|
| 6107 | status open
|
---|
| 6108 |
|
---|
| 6109 | \begin_layout Standard
|
---|
| 6110 |
|
---|
| 6111 |
|
---|
| 6112 | \backslash
|
---|
| 6113 | begin{verbatim}
|
---|
| 6114 | \end_layout
|
---|
| 6115 |
|
---|
| 6116 | \begin_layout Standard
|
---|
| 6117 |
|
---|
| 6118 | ientyp = 0
|
---|
| 6119 | \end_layout
|
---|
| 6120 |
|
---|
| 6121 | \begin_layout Standard
|
---|
| 6122 |
|
---|
| 6123 | sh2 = .false.
|
---|
| 6124 |
|
---|
| 6125 | \end_layout
|
---|
| 6126 |
|
---|
| 6127 | \begin_layout Standard
|
---|
| 6128 |
|
---|
| 6129 | itysol = 0
|
---|
| 6130 | \end_layout
|
---|
| 6131 |
|
---|
| 6132 | \begin_layout Standard
|
---|
| 6133 |
|
---|
| 6134 | iabin = 1
|
---|
| 6135 | \end_layout
|
---|
| 6136 |
|
---|
| 6137 | \begin_layout Standard
|
---|
| 6138 |
|
---|
| 6139 |
|
---|
| 6140 | \backslash
|
---|
| 6141 | end{verbatim}
|
---|
| 6142 | \end_layout
|
---|
| 6143 |
|
---|
| 6144 | \end_inset
|
---|
| 6145 |
|
---|
| 6146 |
|
---|
| 6147 | \end_layout
|
---|
| 6148 |
|
---|
| 6149 | \begin_layout Standard
|
---|
| 6150 | The simulation has a total of 100,000 Monte Carlo sweeps and the multicanonical
|
---|
| 6151 | parameters are updated every 2,000 sweeps.
|
---|
| 6152 | The parameters are calculated from scratch, and we attempt to obtain a
|
---|
| 6153 | histogram in energy in the interval [-12,20] Kcal/mol with energy bin size
|
---|
| 6154 | 1 Kcal/mol.
|
---|
| 6155 | We expect that at temperature 1000 K we are clearly in the high-energy
|
---|
| 6156 | phase where successive configurations have little correlation.
|
---|
| 6157 | This leads to the following set of arguments for calling
|
---|
| 6158 | \emph on
|
---|
| 6159 | mulcan
|
---|
| 6160 | \emph default
|
---|
| 6161 | _
|
---|
| 6162 | \emph on
|
---|
| 6163 | par
|
---|
| 6164 | \emph default
|
---|
| 6165 | :
|
---|
| 6166 | \end_layout
|
---|
| 6167 |
|
---|
| 6168 | \begin_layout Standard
|
---|
| 6169 | \begin_inset ERT
|
---|
| 6170 | status open
|
---|
| 6171 |
|
---|
| 6172 | \begin_layout Standard
|
---|
| 6173 |
|
---|
| 6174 |
|
---|
| 6175 | \backslash
|
---|
| 6176 | begin{verbatim}
|
---|
| 6177 | \end_layout
|
---|
| 6178 |
|
---|
| 6179 | \begin_layout Standard
|
---|
| 6180 |
|
---|
| 6181 | l_iter=.false.
|
---|
| 6182 | \end_layout
|
---|
| 6183 |
|
---|
| 6184 | \begin_layout Standard
|
---|
| 6185 |
|
---|
| 6186 | kmin=-12
|
---|
| 6187 | \end_layout
|
---|
| 6188 |
|
---|
| 6189 | \begin_layout Standard
|
---|
| 6190 |
|
---|
| 6191 | kmax=20
|
---|
| 6192 | \end_layout
|
---|
| 6193 |
|
---|
| 6194 | \begin_layout Standard
|
---|
| 6195 |
|
---|
| 6196 | ebin=1.0d0
|
---|
| 6197 | \end_layout
|
---|
| 6198 |
|
---|
| 6199 | \begin_layout Standard
|
---|
| 6200 |
|
---|
| 6201 | nsweep=100000
|
---|
| 6202 | \end_layout
|
---|
| 6203 |
|
---|
| 6204 | \begin_layout Standard
|
---|
| 6205 |
|
---|
| 6206 | nup=5000
|
---|
| 6207 | \end_layout
|
---|
| 6208 |
|
---|
| 6209 | \begin_layout Standard
|
---|
| 6210 |
|
---|
| 6211 | temp=1000.0
|
---|
| 6212 | \end_layout
|
---|
| 6213 |
|
---|
| 6214 | \begin_layout Standard
|
---|
| 6215 |
|
---|
| 6216 | call mulcan_par(nsweep, nup, temp, kmin, kmax, l_iter)
|
---|
| 6217 | \end_layout
|
---|
| 6218 |
|
---|
| 6219 | \begin_layout Standard
|
---|
| 6220 |
|
---|
| 6221 |
|
---|
| 6222 | \backslash
|
---|
| 6223 | end{verbatim}
|
---|
| 6224 | \end_layout
|
---|
| 6225 |
|
---|
| 6226 | \end_inset
|
---|
| 6227 |
|
---|
| 6228 |
|
---|
| 6229 | \end_layout
|
---|
| 6230 |
|
---|
| 6231 | \begin_layout Standard
|
---|
| 6232 | This example is available in the file
|
---|
| 6233 | \emph on
|
---|
| 6234 | multicanonical.f
|
---|
| 6235 | \emph default
|
---|
| 6236 | in the EXAMPLES directory.
|
---|
| 6237 | After compiling it with
|
---|
| 6238 | \emph on
|
---|
| 6239 | make
|
---|
| 6240 | \emph default
|
---|
| 6241 |
|
---|
| 6242 | \emph on
|
---|
| 6243 | multicanonical
|
---|
| 6244 | \emph default
|
---|
| 6245 | and running the program using
|
---|
| 6246 | \emph on
|
---|
| 6247 | multicanonical
|
---|
| 6248 | \emph default
|
---|
| 6249 | the calculated multicanonical parameters are written into the file '
|
---|
| 6250 | \shape italic
|
---|
| 6251 | muca.d
|
---|
| 6252 | \shape default
|
---|
| 6253 | '.
|
---|
| 6254 | For further iteration of these parameters additional quantities such as
|
---|
| 6255 | the accumulated histogram are written into a file '
|
---|
| 6256 | \shape italic
|
---|
| 6257 | mpar_full.d
|
---|
| 6258 | \shape default
|
---|
| 6259 | ' (out of which '
|
---|
| 6260 | \shape italic
|
---|
| 6261 | mulcan_par
|
---|
| 6262 | \shape default
|
---|
| 6263 | ' reads them if '
|
---|
| 6264 | \shape italic
|
---|
| 6265 | l_iter=.true.
|
---|
| 6266 | \shape default
|
---|
| 6267 | ' is set).
|
---|
| 6268 | We show here only the file '
|
---|
| 6269 | \shape italic
|
---|
| 6270 | muca.d
|
---|
| 6271 | \shape default
|
---|
| 6272 | ' which lists the index of the energy bin, the
|
---|
| 6273 | \begin_inset Formula $\beta(E)$
|
---|
| 6274 | \end_inset
|
---|
| 6275 |
|
---|
| 6276 | and the
|
---|
| 6277 | \begin_inset Formula $\alpha(E)$
|
---|
| 6278 | \end_inset
|
---|
| 6279 |
|
---|
| 6280 | parameters (see
|
---|
| 6281 | \begin_inset LatexCommand citep
|
---|
| 6282 | key "Eisenmenger2001"
|
---|
| 6283 |
|
---|
| 6284 | \end_inset
|
---|
| 6285 |
|
---|
| 6286 | ) for more detailed explanations and references on multicanonical simulations):
|
---|
| 6287 | \end_layout
|
---|
| 6288 |
|
---|
| 6289 | \begin_layout Standard
|
---|
| 6290 | \begin_inset ERT
|
---|
| 6291 | status open
|
---|
| 6292 |
|
---|
| 6293 | \begin_layout Standard
|
---|
| 6294 |
|
---|
| 6295 |
|
---|
| 6296 | \backslash
|
---|
| 6297 | begin{verbatim}
|
---|
| 6298 | \end_layout
|
---|
| 6299 |
|
---|
| 6300 | \begin_layout Standard
|
---|
| 6301 |
|
---|
| 6302 | -12 11.8671041270715 93.0982188015155
|
---|
| 6303 | \end_layout
|
---|
| 6304 |
|
---|
| 6305 | \begin_layout Standard
|
---|
| 6306 |
|
---|
| 6307 | -11 6.74942546567488 34.2449141954539
|
---|
| 6308 | \end_layout
|
---|
| 6309 |
|
---|
| 6310 | \begin_layout Standard
|
---|
| 6311 |
|
---|
| 6312 | -10 4.76239638525333 13.3811088510276
|
---|
| 6313 | \end_layout
|
---|
| 6314 |
|
---|
| 6315 | \begin_layout Standard
|
---|
| 6316 |
|
---|
| 6317 | -9 2.62566106761319 -6.91787666655369
|
---|
| 6318 | \end_layout
|
---|
| 6319 |
|
---|
| 6320 | \begin_layout Standard
|
---|
| 6321 |
|
---|
| 6322 | -8 2.76891298156071 -5.70023539799973
|
---|
| 6323 | \end_layout
|
---|
| 6324 |
|
---|
| 6325 | \begin_layout Standard
|
---|
| 6326 |
|
---|
| 6327 | -7 2.98636199792932 -4.06936777523520
|
---|
| 6328 | \end_layout
|
---|
| 6329 |
|
---|
| 6330 | \begin_layout Standard
|
---|
| 6331 |
|
---|
| 6332 | -6 2.62458524605883 -6.42091666239336
|
---|
| 6333 | \end_layout
|
---|
| 6334 |
|
---|
| 6335 | \begin_layout Standard
|
---|
| 6336 |
|
---|
| 6337 | -5 2.68953283146133 -6.06370494267963
|
---|
| 6338 | \end_layout
|
---|
| 6339 |
|
---|
| 6340 | \begin_layout Standard
|
---|
| 6341 |
|
---|
| 6342 | -4 1.99405651648455 -9.19334836007513
|
---|
| 6343 | \end_layout
|
---|
| 6344 |
|
---|
| 6345 | \begin_layout Standard
|
---|
| 6346 |
|
---|
| 6347 | -3 2.37207855308226 -7.87027123198313
|
---|
| 6348 | \end_layout
|
---|
| 6349 |
|
---|
| 6350 | \begin_layout Standard
|
---|
| 6351 |
|
---|
| 6352 | -2 1.80430850778520 -9.28969634522579
|
---|
| 6353 | \end_layout
|
---|
| 6354 |
|
---|
| 6355 | \begin_layout Standard
|
---|
| 6356 |
|
---|
| 6357 | -1 1.91571656031594 -9.12258426642968
|
---|
| 6358 | \end_layout
|
---|
| 6359 |
|
---|
| 6360 | \begin_layout Standard
|
---|
| 6361 |
|
---|
| 6362 | 0 1.72752866077015 -9.21667821620257
|
---|
| 6363 | \end_layout
|
---|
| 6364 |
|
---|
| 6365 | \begin_layout Standard
|
---|
| 6366 |
|
---|
| 6367 | 1 1.66881722525666 -9.18732249844583
|
---|
| 6368 | \end_layout
|
---|
| 6369 |
|
---|
| 6370 | \begin_layout Standard
|
---|
| 6371 |
|
---|
| 6372 | 2 1.50004119691055 -8.93415845592665
|
---|
| 6373 | \end_layout
|
---|
| 6374 |
|
---|
| 6375 | \begin_layout Standard
|
---|
| 6376 |
|
---|
| 6377 | 3 1.39142908670518 -8.66262818041324
|
---|
| 6378 | \end_layout
|
---|
| 6379 |
|
---|
| 6380 | \begin_layout Standard
|
---|
| 6381 |
|
---|
| 6382 | 4 1.16605491925085 -7.87381859432308
|
---|
| 6383 | \end_layout
|
---|
| 6384 |
|
---|
| 6385 | \begin_layout Standard
|
---|
| 6386 |
|
---|
| 6387 | 5 1.88002935687926 -11.0867035636509
|
---|
| 6388 | \end_layout
|
---|
| 6389 |
|
---|
| 6390 | \begin_layout Standard
|
---|
| 6391 |
|
---|
| 6392 | 6 0.784923700785834 -5.06362245513708
|
---|
| 6393 | \end_layout
|
---|
| 6394 |
|
---|
| 6395 | \begin_layout Standard
|
---|
| 6396 |
|
---|
| 6397 | 7 1.15928001690741 -7.49693850992732
|
---|
| 6398 | \end_layout
|
---|
| 6399 |
|
---|
| 6400 | \begin_layout Standard
|
---|
| 6401 |
|
---|
| 6402 | 8 1.53630835441332 -10.3246510412217
|
---|
| 6403 | \end_layout
|
---|
| 6404 |
|
---|
| 6405 | \begin_layout Standard
|
---|
| 6406 |
|
---|
| 6407 | 9 0.804876443148135 -4.10747979546758
|
---|
| 6408 | \end_layout
|
---|
| 6409 |
|
---|
| 6410 | \begin_layout Standard
|
---|
| 6411 |
|
---|
| 6412 | 10 1.20439627142663 -7.90291816411324
|
---|
| 6413 | \end_layout
|
---|
| 6414 |
|
---|
| 6415 | \begin_layout Standard
|
---|
| 6416 |
|
---|
| 6417 | 11 0.843296201282429 -4.11136742759918
|
---|
| 6418 | \end_layout
|
---|
| 6419 |
|
---|
| 6420 | \begin_layout Standard
|
---|
| 6421 |
|
---|
| 6422 | 12 1.03327436670481 -6.29611632995659
|
---|
| 6423 | \end_layout
|
---|
| 6424 |
|
---|
| 6425 | \begin_layout Standard
|
---|
| 6426 |
|
---|
| 6427 | 13 0.847836723791197 -3.97814579353639
|
---|
| 6428 | \end_layout
|
---|
| 6429 |
|
---|
| 6430 | \begin_layout Standard
|
---|
| 6431 |
|
---|
| 6432 | 14 0.794466332096526 -3.25764550565833
|
---|
| 6433 | \end_layout
|
---|
| 6434 |
|
---|
| 6435 | \begin_layout Standard
|
---|
| 6436 |
|
---|
| 6437 | 15 0.665347460625295 -1.38542186932548
|
---|
| 6438 | \end_layout
|
---|
| 6439 |
|
---|
| 6440 | \begin_layout Standard
|
---|
| 6441 |
|
---|
| 6442 | 16 0.897108190646473 -4.97771318465375
|
---|
| 6443 | \end_layout
|
---|
| 6444 |
|
---|
| 6445 | \begin_layout Standard
|
---|
| 6446 |
|
---|
| 6447 | 17 0.527634627532446 1.11860060672770
|
---|
| 6448 | \end_layout
|
---|
| 6449 |
|
---|
| 6450 | \begin_layout Standard
|
---|
| 6451 |
|
---|
| 6452 | 18 0.591554662202600 0.000000000000000E+000
|
---|
| 6453 | \end_layout
|
---|
| 6454 |
|
---|
| 6455 | \begin_layout Standard
|
---|
| 6456 |
|
---|
| 6457 | 19 0.591554662202600 0.000000000000000E+000
|
---|
| 6458 | \end_layout
|
---|
| 6459 |
|
---|
| 6460 | \begin_layout Standard
|
---|
| 6461 |
|
---|
| 6462 | 20 0.591554662202600 0.000000000000000E+000
|
---|
| 6463 | \end_layout
|
---|
| 6464 |
|
---|
| 6465 | \begin_layout Standard
|
---|
| 6466 |
|
---|
| 6467 |
|
---|
| 6468 | \backslash
|
---|
| 6469 | end{verbatim}
|
---|
| 6470 | \end_layout
|
---|
| 6471 |
|
---|
| 6472 | \end_inset
|
---|
| 6473 |
|
---|
| 6474 |
|
---|
| 6475 | \end_layout
|
---|
| 6476 |
|
---|
| 6477 | \begin_layout Standard
|
---|
| 6478 | A test simulation of 100,000 Monte Carlo sweeps (using subroutine '
|
---|
| 6479 | \shape italic
|
---|
| 6480 | mulcan_sim
|
---|
| 6481 | \shape default
|
---|
| 6482 | ' with these weights led to the following histogram that is flat over the
|
---|
| 6483 | studied energy range (as is characteristic for the multicanonical ensemble)
|
---|
| 6484 | (note that the last energy bin contains all entries for energies larger/equal
|
---|
| 6485 | than 20 Kcal/mol):
|
---|
| 6486 | \end_layout
|
---|
| 6487 |
|
---|
| 6488 | \begin_layout Standard
|
---|
| 6489 | \begin_inset ERT
|
---|
| 6490 | status open
|
---|
| 6491 |
|
---|
| 6492 | \begin_layout Standard
|
---|
| 6493 |
|
---|
| 6494 |
|
---|
| 6495 | \backslash
|
---|
| 6496 | begin{verbatim}
|
---|
| 6497 | \end_layout
|
---|
| 6498 |
|
---|
| 6499 | \begin_layout Standard
|
---|
| 6500 |
|
---|
| 6501 | -9 105
|
---|
| 6502 | \end_layout
|
---|
| 6503 |
|
---|
| 6504 | \begin_layout Standard
|
---|
| 6505 |
|
---|
| 6506 | -8 828
|
---|
| 6507 | \end_layout
|
---|
| 6508 |
|
---|
| 6509 | \begin_layout Standard
|
---|
| 6510 |
|
---|
| 6511 | -7 1945
|
---|
| 6512 | \end_layout
|
---|
| 6513 |
|
---|
| 6514 | \begin_layout Standard
|
---|
| 6515 |
|
---|
| 6516 | -6 3108
|
---|
| 6517 | \end_layout
|
---|
| 6518 |
|
---|
| 6519 | \begin_layout Standard
|
---|
| 6520 |
|
---|
| 6521 | -5 3247
|
---|
| 6522 | \end_layout
|
---|
| 6523 |
|
---|
| 6524 | \begin_layout Standard
|
---|
| 6525 |
|
---|
| 6526 | -4 3054
|
---|
| 6527 | \end_layout
|
---|
| 6528 |
|
---|
| 6529 | \begin_layout Standard
|
---|
| 6530 |
|
---|
| 6531 | -3 2844
|
---|
| 6532 | \end_layout
|
---|
| 6533 |
|
---|
| 6534 | \begin_layout Standard
|
---|
| 6535 |
|
---|
| 6536 | -2 2531
|
---|
| 6537 | \end_layout
|
---|
| 6538 |
|
---|
| 6539 | \begin_layout Standard
|
---|
| 6540 |
|
---|
| 6541 | -1 2397
|
---|
| 6542 | \end_layout
|
---|
| 6543 |
|
---|
| 6544 | \begin_layout Standard
|
---|
| 6545 |
|
---|
| 6546 | 0 2082
|
---|
| 6547 | \end_layout
|
---|
| 6548 |
|
---|
| 6549 | \begin_layout Standard
|
---|
| 6550 |
|
---|
| 6551 | 1 2179
|
---|
| 6552 | \end_layout
|
---|
| 6553 |
|
---|
| 6554 | \begin_layout Standard
|
---|
| 6555 |
|
---|
| 6556 | 2 2294
|
---|
| 6557 | \end_layout
|
---|
| 6558 |
|
---|
| 6559 | \begin_layout Standard
|
---|
| 6560 |
|
---|
| 6561 | 3 2579
|
---|
| 6562 | \end_layout
|
---|
| 6563 |
|
---|
| 6564 | \begin_layout Standard
|
---|
| 6565 |
|
---|
| 6566 | 4 3193
|
---|
| 6567 | \end_layout
|
---|
| 6568 |
|
---|
| 6569 | \begin_layout Standard
|
---|
| 6570 |
|
---|
| 6571 | 5 2855
|
---|
| 6572 | \end_layout
|
---|
| 6573 |
|
---|
| 6574 | \begin_layout Standard
|
---|
| 6575 |
|
---|
| 6576 | 6 2927
|
---|
| 6577 | \end_layout
|
---|
| 6578 |
|
---|
| 6579 | \begin_layout Standard
|
---|
| 6580 |
|
---|
| 6581 | 7 3994
|
---|
| 6582 | \end_layout
|
---|
| 6583 |
|
---|
| 6584 | \begin_layout Standard
|
---|
| 6585 |
|
---|
| 6586 | 8 3362
|
---|
| 6587 | \end_layout
|
---|
| 6588 |
|
---|
| 6589 | \begin_layout Standard
|
---|
| 6590 |
|
---|
| 6591 | 9 3047
|
---|
| 6592 | \end_layout
|
---|
| 6593 |
|
---|
| 6594 | \begin_layout Standard
|
---|
| 6595 |
|
---|
| 6596 | 10 3289
|
---|
| 6597 | \end_layout
|
---|
| 6598 |
|
---|
| 6599 | \begin_layout Standard
|
---|
| 6600 |
|
---|
| 6601 | 11 3199
|
---|
| 6602 | \end_layout
|
---|
| 6603 |
|
---|
| 6604 | \begin_layout Standard
|
---|
| 6605 |
|
---|
| 6606 | 12 3412
|
---|
| 6607 | \end_layout
|
---|
| 6608 |
|
---|
| 6609 | \begin_layout Standard
|
---|
| 6610 |
|
---|
| 6611 | 13 3034
|
---|
| 6612 | \end_layout
|
---|
| 6613 |
|
---|
| 6614 | \begin_layout Standard
|
---|
| 6615 |
|
---|
| 6616 | 14 3092
|
---|
| 6617 | \end_layout
|
---|
| 6618 |
|
---|
| 6619 | \begin_layout Standard
|
---|
| 6620 |
|
---|
| 6621 | 15 3258
|
---|
| 6622 | \end_layout
|
---|
| 6623 |
|
---|
| 6624 | \begin_layout Standard
|
---|
| 6625 |
|
---|
| 6626 | 16 3079
|
---|
| 6627 | \end_layout
|
---|
| 6628 |
|
---|
| 6629 | \begin_layout Standard
|
---|
| 6630 |
|
---|
| 6631 | 17 2957
|
---|
| 6632 | \end_layout
|
---|
| 6633 |
|
---|
| 6634 | \begin_layout Standard
|
---|
| 6635 |
|
---|
| 6636 | 18 3157
|
---|
| 6637 | \end_layout
|
---|
| 6638 |
|
---|
| 6639 | \begin_layout Standard
|
---|
| 6640 |
|
---|
| 6641 | 19 3055
|
---|
| 6642 | \end_layout
|
---|
| 6643 |
|
---|
| 6644 | \begin_layout Standard
|
---|
| 6645 |
|
---|
| 6646 | 20 19897
|
---|
| 6647 | \end_layout
|
---|
| 6648 |
|
---|
| 6649 | \begin_layout Standard
|
---|
| 6650 |
|
---|
| 6651 |
|
---|
| 6652 | \backslash
|
---|
| 6653 | end{verbatim}
|
---|
| 6654 | \end_layout
|
---|
| 6655 |
|
---|
| 6656 | \end_inset
|
---|
| 6657 |
|
---|
| 6658 |
|
---|
| 6659 | \end_layout
|
---|
| 6660 |
|
---|
| 6661 | \begin_layout Subsection
|
---|
| 6662 | Regularization of the B domain of protein A
|
---|
| 6663 | \begin_inset LatexCommand label
|
---|
| 6664 | name "sub:Regularization-of-the"
|
---|
| 6665 |
|
---|
| 6666 | \end_inset
|
---|
| 6667 |
|
---|
| 6668 |
|
---|
| 6669 | \end_layout
|
---|
| 6670 |
|
---|
| 6671 | \begin_layout Standard
|
---|
| 6672 | Frequently, one wants to compare the results of a simulation with experimental
|
---|
| 6673 | data.
|
---|
| 6674 | When we compare properties of calculated configurations with those of structure
|
---|
| 6675 | s from the Protein Data Bank (PDB), we have to remember that the actual
|
---|
| 6676 | bond lengths and angles in the PDB-structure will differ from the fixed
|
---|
| 6677 | values that are assumed with the ECEPP, FLEX, and Lund potentials.
|
---|
| 6678 | Forcing the molecule into the standard bonding geometry model may lead
|
---|
| 6679 | to un-physically high energies.
|
---|
| 6680 | The process of finding an optimal structure within the standard geometry
|
---|
| 6681 | model starting from a PDB-structure is called regularization.
|
---|
| 6682 | \end_layout
|
---|
| 6683 |
|
---|
| 6684 | \begin_layout Standard
|
---|
| 6685 | In our example, we regularize of the coordinates for residues 10-55 of the
|
---|
| 6686 | B domain of
|
---|
| 6687 | \shape italic
|
---|
| 6688 | Staphylococcus Aureus
|
---|
| 6689 | \shape default
|
---|
| 6690 | Protein A, which were taken from entry
|
---|
| 6691 | \shape italic
|
---|
| 6692 | 1BDD
|
---|
| 6693 | \shape default
|
---|
| 6694 | of the Protein Data Bank (see
|
---|
| 6695 | \begin_inset LatexCommand url
|
---|
| 6696 | target "http://www.rcsb.org"
|
---|
| 6697 |
|
---|
| 6698 | \end_inset
|
---|
| 6699 |
|
---|
| 6700 | ), as provided with this package in file
|
---|
| 6701 | \shape italic
|
---|
| 6702 | 1bdd.pdb
|
---|
| 6703 | \shape default
|
---|
| 6704 | .
|
---|
| 6705 | Setting the variable '
|
---|
| 6706 | \shape italic
|
---|
| 6707 | iabin = 0
|
---|
| 6708 | \shape default
|
---|
| 6709 | ' in
|
---|
| 6710 | \shape italic
|
---|
| 6711 | main.f
|
---|
| 6712 | \shape default
|
---|
| 6713 | makes
|
---|
| 6714 | \shape italic
|
---|
| 6715 | init_molecule
|
---|
| 6716 | \shape default
|
---|
| 6717 | call subroutine
|
---|
| 6718 | \shape italic
|
---|
| 6719 | pdbread
|
---|
| 6720 | \shape default
|
---|
| 6721 | that reads the amino acid sequence and the atomic coordinates from the
|
---|
| 6722 | PDB- structure and stores this data in arrays declared in '
|
---|
| 6723 | \shape italic
|
---|
| 6724 | INCP.H
|
---|
| 6725 | \shape default
|
---|
| 6726 | '.
|
---|
| 6727 | Then
|
---|
| 6728 | \shape italic
|
---|
| 6729 | pdbvars
|
---|
| 6730 | \shape default
|
---|
| 6731 | is automatically called to measure all dihedral angles.
|
---|
| 6732 | In order to regularize the PDB-structure one has to
|
---|
| 6733 | \shape italic
|
---|
| 6734 | call regul(nml, iter, nsteps,
|
---|
| 6735 | \begin_inset Formula $\varepsilon$
|
---|
| 6736 | \end_inset
|
---|
| 6737 |
|
---|
| 6738 | )
|
---|
| 6739 | \shape default
|
---|
| 6740 | as the task subroutine in '
|
---|
| 6741 | \shape italic
|
---|
| 6742 | main
|
---|
| 6743 | \shape default
|
---|
| 6744 | ' .
|
---|
| 6745 | Set the following parameters in '
|
---|
| 6746 | \shape italic
|
---|
| 6747 | main
|
---|
| 6748 | \shape default
|
---|
| 6749 | ', accordingly:
|
---|
| 6750 | \newline
|
---|
| 6751 |
|
---|
| 6752 | \newline
|
---|
| 6753 |
|
---|
| 6754 | \shape italic
|
---|
| 6755 | ientyp=0
|
---|
| 6756 | \newline
|
---|
| 6757 | sh2 = .false.
|
---|
| 6758 | \newline
|
---|
| 6759 | itysol = 0
|
---|
| 6760 | \newline
|
---|
| 6761 | iabin = 0
|
---|
| 6762 | \shape default
|
---|
| 6763 |
|
---|
| 6764 | \newline
|
---|
| 6765 |
|
---|
| 6766 | \newline
|
---|
| 6767 | Note that '
|
---|
| 6768 | \shape italic
|
---|
| 6769 | regul
|
---|
| 6770 | \shape default
|
---|
| 6771 | ', as any other task subroutine, has to be called AFTER '
|
---|
| 6772 | \shape italic
|
---|
| 6773 | init_molecule
|
---|
| 6774 | \shape default
|
---|
| 6775 | ' .
|
---|
| 6776 | The example is available in the EXAMPLES directory.
|
---|
| 6777 | You can compile it by calling
|
---|
| 6778 | \emph on
|
---|
| 6779 | make regularization.
|
---|
| 6780 |
|
---|
| 6781 | \emph default
|
---|
| 6782 | Run the program by calling
|
---|
| 6783 | \emph on
|
---|
| 6784 | regularization
|
---|
| 6785 | \emph default
|
---|
| 6786 | .
|
---|
| 6787 | We use 10 iterations with up to 15000 sweeps each and
|
---|
| 6788 | \begin_inset Formula $\varepsilon=10^{-7}$
|
---|
| 6789 | \end_inset
|
---|
| 6790 |
|
---|
| 6791 | .
|
---|
| 6792 | A value for
|
---|
| 6793 | \begin_inset Formula $\varepsilon$
|
---|
| 6794 | \end_inset
|
---|
| 6795 |
|
---|
| 6796 | that is too large may lead to numerical instabilities.
|
---|
| 6797 |
|
---|
| 6798 | \end_layout
|
---|
| 6799 |
|
---|
| 6800 | \begin_layout Standard
|
---|
| 6801 | First '
|
---|
| 6802 | \shape italic
|
---|
| 6803 | regul
|
---|
| 6804 | \shape default
|
---|
| 6805 | ' obtains its input from the arrays declared in '
|
---|
| 6806 | \shape italic
|
---|
| 6807 | INCP.H
|
---|
| 6808 | \shape default
|
---|
| 6809 | '.
|
---|
| 6810 | In a first step a naive representation of the molecule is build in the
|
---|
| 6811 | ECEPP geometry from the stored dihedral angles that were calculated from
|
---|
| 6812 | the PDB coordinates.
|
---|
| 6813 | This simple model serves as starting configuration for the regularization.
|
---|
| 6814 | In our example, its root-mean-square deviation (over all heave atoms) compared
|
---|
| 6815 | to the PDB-structure initially is 2.8
|
---|
| 6816 | \begin_inset ERT
|
---|
| 6817 | status collapsed
|
---|
| 6818 |
|
---|
| 6819 | \begin_layout Standard
|
---|
| 6820 |
|
---|
| 6821 |
|
---|
| 6822 | \backslash
|
---|
| 6823 | AA
|
---|
| 6824 | \end_layout
|
---|
| 6825 |
|
---|
| 6826 | \end_inset
|
---|
| 6827 |
|
---|
| 6828 | and its ECEPP-energy
|
---|
| 6829 | \begin_inset Formula $\approx10^{5}$
|
---|
| 6830 | \end_inset
|
---|
| 6831 |
|
---|
| 6832 | kcal/mol, mainly due to excessive van-der-Waals repulsions.
|
---|
| 6833 | The regularization starts by first minimizing a term that measures the
|
---|
| 6834 | sum of squared distances between heavy atoms in the SMMP-structure and
|
---|
| 6835 | the given PDB-structure.
|
---|
| 6836 | This leads to a rmsd of 0.14
|
---|
| 6837 | \begin_inset ERT
|
---|
| 6838 | status collapsed
|
---|
| 6839 |
|
---|
| 6840 | \begin_layout Standard
|
---|
| 6841 |
|
---|
| 6842 |
|
---|
| 6843 | \backslash
|
---|
| 6844 | AA
|
---|
| 6845 | \end_layout
|
---|
| 6846 |
|
---|
| 6847 | \end_inset
|
---|
| 6848 |
|
---|
| 6849 | .
|
---|
| 6850 | After this initial step a list of bad contacts (vdW-energy of more than
|
---|
| 6851 | 2 kcal/mol) in the SMMP-structure is printed out.
|
---|
| 6852 | In a second step the physical energy is minimized, allowing only the free
|
---|
| 6853 | hydrogens to move, and the bad contacts and rmsd are displayed again.
|
---|
| 6854 | This step reduces the ECEPP-energy to
|
---|
| 6855 | \begin_inset Formula $\approx10^{3}$
|
---|
| 6856 | \end_inset
|
---|
| 6857 |
|
---|
| 6858 | kcal/mol.
|
---|
| 6859 | '
|
---|
| 6860 | \shape italic
|
---|
| 6861 | Regul
|
---|
| 6862 | \shape default
|
---|
| 6863 | ' aims at further reducing this energy while at the same time keeping the
|
---|
| 6864 | rmsd as small as possible.
|
---|
| 6865 | This is done by minimizing a composite energy from the weighted sum of
|
---|
| 6866 | physical ECEPP-energy and constraint energy (the quadratic distance measure)
|
---|
| 6867 | over 10 iterations.
|
---|
| 6868 | In each iteration the weight of the constraint energy is successively lowered
|
---|
| 6869 | (from 1 to 0) and the weight of the ECEPP energy raised (from 0 to 1).
|
---|
| 6870 | At the end, the dihedral angles of the final structure are printed out
|
---|
| 6871 | together with its rmsd and a list of (eventually) remaining bad contacts.
|
---|
| 6872 | \end_layout
|
---|
| 6873 |
|
---|
| 6874 | \begin_layout Standard
|
---|
| 6875 | The following output is obtained from this last iteration with a weight
|
---|
| 6876 | of 1 for the ECEPP-energy and a weight of 0 for the constraint energy,
|
---|
| 6877 | that leads to a SMMP-configuration with a total ECEPP-energy of
|
---|
| 6878 | \begin_inset Formula $-429.9$
|
---|
| 6879 | \end_inset
|
---|
| 6880 |
|
---|
| 6881 | kcal/mol and a rmsd of 1.89
|
---|
| 6882 | \begin_inset ERT
|
---|
| 6883 | status inlined
|
---|
| 6884 |
|
---|
| 6885 | \begin_layout Standard
|
---|
| 6886 |
|
---|
| 6887 |
|
---|
| 6888 | \backslash
|
---|
| 6889 | AA
|
---|
| 6890 | \end_layout
|
---|
| 6891 |
|
---|
| 6892 | \end_inset
|
---|
| 6893 |
|
---|
| 6894 | , compared to the PDB-structure:
|
---|
| 6895 | \end_layout
|
---|
| 6896 |
|
---|
| 6897 | \begin_layout Standard
|
---|
| 6898 | \begin_inset ERT
|
---|
| 6899 | status open
|
---|
| 6900 |
|
---|
| 6901 | \begin_layout Standard
|
---|
| 6902 |
|
---|
| 6903 |
|
---|
| 6904 | \backslash
|
---|
| 6905 | begin{verbatim}
|
---|
| 6906 | \end_layout
|
---|
| 6907 |
|
---|
| 6908 | \begin_layout Standard
|
---|
| 6909 |
|
---|
| 6910 | ================ Minimization #10 Wt(energy) = 0.100E+01 Wt(regul.)
|
---|
| 6911 | = 0.000E+00
|
---|
| 6912 | \end_layout
|
---|
| 6913 |
|
---|
| 6914 | \begin_layout Standard
|
---|
| 6915 |
|
---|
| 6916 | \end_layout
|
---|
| 6917 |
|
---|
| 6918 | \begin_layout Standard
|
---|
| 6919 |
|
---|
| 6920 | \end_layout
|
---|
| 6921 |
|
---|
| 6922 | \begin_layout Standard
|
---|
| 6923 |
|
---|
| 6924 | Energy BEFORE minimization:
|
---|
| 6925 | \end_layout
|
---|
| 6926 |
|
---|
| 6927 | \begin_layout Standard
|
---|
| 6928 |
|
---|
| 6929 | \end_layout
|
---|
| 6930 |
|
---|
| 6931 | \begin_layout Standard
|
---|
| 6932 |
|
---|
| 6933 | Total: -0.39831E+03
|
---|
| 6934 | \end_layout
|
---|
| 6935 |
|
---|
| 6936 | \begin_layout Standard
|
---|
| 6937 |
|
---|
| 6938 | Coulomb: -0.4685E+02 Lennard-Jones: -0.3306E+03 HB: -0.6915E+02
|
---|
| 6939 | \end_layout
|
---|
| 6940 |
|
---|
| 6941 | \begin_layout Standard
|
---|
| 6942 |
|
---|
| 6943 | Variables: 0.4831E+02 Solvatation: 0.0000E+00 Regularization: 0.3315E+03
|
---|
| 6944 | \end_layout
|
---|
| 6945 |
|
---|
| 6946 | \begin_layout Standard
|
---|
| 6947 |
|
---|
| 6948 | \end_layout
|
---|
| 6949 |
|
---|
| 6950 | \begin_layout Standard
|
---|
| 6951 |
|
---|
| 6952 | Step 1: energy 0.259565E+13 ( 0.296722E+30, 0.363456E+12 )
|
---|
| 6953 | \end_layout
|
---|
| 6954 |
|
---|
| 6955 | \begin_layout Standard
|
---|
| 6956 |
|
---|
| 6957 | Step 2: energy 0.481884E+09 ( 0.572102E+22, 0.644342E+12 )
|
---|
| 6958 | \end_layout
|
---|
| 6959 |
|
---|
| 6960 | \begin_layout Standard
|
---|
| 6961 |
|
---|
| 6962 | Step 3: energy 0.444100E+10 ( 0.599018E+24, 0.617413E+12 )
|
---|
| 6963 | \end_layout
|
---|
| 6964 |
|
---|
| 6965 | \begin_layout Standard
|
---|
| 6966 |
|
---|
| 6967 | Step 4: energy 0.491253E+10 ( 0.220900E+25, 0.533540E+12 )
|
---|
| 6968 | \end_layout
|
---|
| 6969 |
|
---|
| 6970 | \begin_layout Standard
|
---|
| 6971 |
|
---|
| 6972 | Step 5: energy -0.355950E+03 ( 0.341264E+06, 0.495213E+10 )
|
---|
| 6973 | \end_layout
|
---|
| 6974 |
|
---|
| 6975 | \begin_layout Standard
|
---|
| 6976 |
|
---|
| 6977 | Step 6: energy -0.395467E+03 ( 0.762827E+06, 0.726715E+08 )
|
---|
| 6978 | \end_layout
|
---|
| 6979 |
|
---|
| 6980 | \begin_layout Standard
|
---|
| 6981 |
|
---|
| 6982 | Step 7: energy -0.398489E+03 ( 0.198935E+05, 0.137122E+08 )
|
---|
| 6983 | \end_layout
|
---|
| 6984 |
|
---|
| 6985 | \begin_layout Standard
|
---|
| 6986 |
|
---|
| 6987 | Step 8: energy -0.398761E+03 ( 0.409017E+05, 0.187175E+08 )
|
---|
| 6988 | \end_layout
|
---|
| 6989 |
|
---|
| 6990 | \begin_layout Standard
|
---|
| 6991 |
|
---|
| 6992 | Step 9: energy -0.399231E+03 ( 0.197834E+05, 0.329551E+08 )
|
---|
| 6993 | \end_layout
|
---|
| 6994 |
|
---|
| 6995 | \begin_layout Standard
|
---|
| 6996 |
|
---|
| 6997 | Step 10: energy -0.399787E+03 ( 0.143934E+06, 0.121392E+09 )
|
---|
| 6998 | \end_layout
|
---|
| 6999 |
|
---|
| 7000 | \begin_layout Standard
|
---|
| 7001 |
|
---|
| 7002 | ...
|
---|
| 7003 | \end_layout
|
---|
| 7004 |
|
---|
| 7005 | \begin_layout Standard
|
---|
| 7006 |
|
---|
| 7007 | ...
|
---|
| 7008 | \end_layout
|
---|
| 7009 |
|
---|
| 7010 | \begin_layout Standard
|
---|
| 7011 |
|
---|
| 7012 | ...
|
---|
| 7013 | \end_layout
|
---|
| 7014 |
|
---|
| 7015 | \begin_layout Standard
|
---|
| 7016 |
|
---|
| 7017 | Step 415: energy -0.429868E+03 ( 0.135007E-03, 0.523386E+11 )
|
---|
| 7018 | \end_layout
|
---|
| 7019 |
|
---|
| 7020 | \begin_layout Standard
|
---|
| 7021 |
|
---|
| 7022 | Step 416: energy -0.429868E+03 ( 0.123681E-04, 0.523385E+11 )
|
---|
| 7023 | \end_layout
|
---|
| 7024 |
|
---|
| 7025 | \begin_layout Standard
|
---|
| 7026 |
|
---|
| 7027 | Step 417: energy -0.429868E+03 ( 0.254870E-05, 0.523385E+11 )
|
---|
| 7028 | \end_layout
|
---|
| 7029 |
|
---|
| 7030 | \begin_layout Standard
|
---|
| 7031 |
|
---|
| 7032 | Step 418: energy -0.429868E+03 ( 0.193334E-05, 0.523385E+11 )
|
---|
| 7033 | \end_layout
|
---|
| 7034 |
|
---|
| 7035 | \begin_layout Standard
|
---|
| 7036 |
|
---|
| 7037 | Step 419: energy -0.429868E+03 ( 0.140748E-05, 0.523385E+11 )
|
---|
| 7038 | \end_layout
|
---|
| 7039 |
|
---|
| 7040 | \begin_layout Standard
|
---|
| 7041 |
|
---|
| 7042 | Step 420: energy -0.429868E+03 ( 0.740869E-06, 0.523384E+11 )
|
---|
| 7043 | \end_layout
|
---|
| 7044 |
|
---|
| 7045 | \begin_layout Standard
|
---|
| 7046 |
|
---|
| 7047 | Step 421: energy -0.429868E+03 ( 0.489693E-06, 0.523384E+11 )
|
---|
| 7048 | \end_layout
|
---|
| 7049 |
|
---|
| 7050 | \begin_layout Standard
|
---|
| 7051 |
|
---|
| 7052 | Step 422: energy -0.429868E+03 ( 0.282056E-06, 0.523384E+11 )
|
---|
| 7053 | \end_layout
|
---|
| 7054 |
|
---|
| 7055 | \begin_layout Standard
|
---|
| 7056 |
|
---|
| 7057 | Step 423: energy -0.429868E+03 ( 0.104563E-06, 0.523384E+11 )
|
---|
| 7058 | \end_layout
|
---|
| 7059 |
|
---|
| 7060 | \begin_layout Standard
|
---|
| 7061 |
|
---|
| 7062 | Step 424: energy -0.429868E+03 ( 0.519142E-07, 0.523385E+11 )
|
---|
| 7063 | \end_layout
|
---|
| 7064 |
|
---|
| 7065 | \begin_layout Standard
|
---|
| 7066 |
|
---|
| 7067 | Step 425: energy -0.429868E+03 ( 0.104563E-06, 0.523384E+11 )
|
---|
| 7068 | \end_layout
|
---|
| 7069 |
|
---|
| 7070 | \begin_layout Standard
|
---|
| 7071 |
|
---|
| 7072 | ---- CONVERGENCE ----
|
---|
| 7073 | \end_layout
|
---|
| 7074 |
|
---|
| 7075 | \begin_layout Standard
|
---|
| 7076 |
|
---|
| 7077 | \end_layout
|
---|
| 7078 |
|
---|
| 7079 | \begin_layout Standard
|
---|
| 7080 |
|
---|
| 7081 | Final energies __________________________________________________
|
---|
| 7082 | \end_layout
|
---|
| 7083 |
|
---|
| 7084 | \begin_layout Standard
|
---|
| 7085 |
|
---|
| 7086 | \end_layout
|
---|
| 7087 |
|
---|
| 7088 | \begin_layout Standard
|
---|
| 7089 |
|
---|
| 7090 | Total: -0.42987E+03
|
---|
| 7091 | \end_layout
|
---|
| 7092 |
|
---|
| 7093 | \begin_layout Standard
|
---|
| 7094 |
|
---|
| 7095 | Coulomb: -0.5431E+02 Lennard-Jones: -0.3510E+03 HB: -0.7268E+02
|
---|
| 7096 | \end_layout
|
---|
| 7097 |
|
---|
| 7098 | \begin_layout Standard
|
---|
| 7099 |
|
---|
| 7100 | Variables: 0.4809E+02 Solvatation: 0.0000E+00 Regularization: 0.2241E+05
|
---|
| 7101 | \end_layout
|
---|
| 7102 |
|
---|
| 7103 | \begin_layout Standard
|
---|
| 7104 |
|
---|
| 7105 | ...
|
---|
| 7106 | \end_layout
|
---|
| 7107 |
|
---|
| 7108 | \begin_layout Standard
|
---|
| 7109 |
|
---|
| 7110 |
|
---|
| 7111 | \end_layout
|
---|
| 7112 |
|
---|
| 7113 | \begin_layout Standard
|
---|
| 7114 |
|
---|
| 7115 | RMSD = 1.89099626258629
|
---|
| 7116 | \end_layout
|
---|
| 7117 |
|
---|
| 7118 | \begin_layout Standard
|
---|
| 7119 |
|
---|
| 7120 | \end_layout
|
---|
| 7121 |
|
---|
| 7122 | \begin_layout Standard
|
---|
| 7123 |
|
---|
| 7124 |
|
---|
| 7125 | \backslash
|
---|
| 7126 | end{verbatim}
|
---|
| 7127 | \end_layout
|
---|
| 7128 |
|
---|
| 7129 | \end_inset
|
---|
| 7130 |
|
---|
| 7131 |
|
---|
| 7132 | \end_layout
|
---|
| 7133 |
|
---|
| 7134 | \begin_layout Subsection
|
---|
| 7135 | Parallel Tempering simulation of four A
|
---|
| 7136 | \begin_inset Formula $\beta_{16-22}$
|
---|
| 7137 | \end_inset
|
---|
| 7138 |
|
---|
| 7139 | peptides
|
---|
| 7140 | \begin_inset LatexCommand label
|
---|
| 7141 | name "sub:Parallel-Tempering-simulation"
|
---|
| 7142 |
|
---|
| 7143 | \end_inset
|
---|
| 7144 |
|
---|
| 7145 |
|
---|
| 7146 | \end_layout
|
---|
| 7147 |
|
---|
| 7148 | \begin_layout Standard
|
---|
| 7149 | In the following example, a parallel tempering simulation of the fragment
|
---|
| 7150 | 16--22 of Alzheimer's
|
---|
| 7151 | \begin_inset Formula $\beta$
|
---|
| 7152 | \end_inset
|
---|
| 7153 |
|
---|
| 7154 | -amyloid in solvent.
|
---|
| 7155 | It relies on the ECEPP/3 force-field and all dihedral angles are free.
|
---|
| 7156 | References for the algorithm can be found in
|
---|
| 7157 | \begin_inset LatexCommand cite
|
---|
| 7158 | key "Eisenmenger2001"
|
---|
| 7159 |
|
---|
| 7160 | \end_inset
|
---|
| 7161 |
|
---|
| 7162 | .
|
---|
| 7163 | The simulation is performed on a parallel computer on
|
---|
| 7164 | \begin_inset Formula $n\times8$
|
---|
| 7165 | \end_inset
|
---|
| 7166 |
|
---|
| 7167 | processors.
|
---|
| 7168 | The example is available in the EXAMPLES directory as
|
---|
| 7169 | \emph on
|
---|
| 7170 | parallel_tempering_p
|
---|
| 7171 | \emph default
|
---|
| 7172 | .
|
---|
| 7173 | Commpile it using
|
---|
| 7174 | \emph on
|
---|
| 7175 | make parallel_tempering
|
---|
| 7176 | \emph default
|
---|
| 7177 | .
|
---|
| 7178 | Set the following parameters
|
---|
| 7179 | \end_layout
|
---|
| 7180 |
|
---|
| 7181 | \begin_layout Standard
|
---|
| 7182 | \begin_inset ERT
|
---|
| 7183 | status open
|
---|
| 7184 |
|
---|
| 7185 | \begin_layout Standard
|
---|
| 7186 |
|
---|
| 7187 |
|
---|
| 7188 | \backslash
|
---|
| 7189 | begin{verbatim}
|
---|
| 7190 | \end_layout
|
---|
| 7191 |
|
---|
| 7192 | \begin_layout Standard
|
---|
| 7193 |
|
---|
| 7194 | num_replica = 8
|
---|
| 7195 | \end_layout
|
---|
| 7196 |
|
---|
| 7197 | \begin_layout Standard
|
---|
| 7198 |
|
---|
| 7199 | ientyp = 0
|
---|
| 7200 | \end_layout
|
---|
| 7201 |
|
---|
| 7202 | \begin_layout Standard
|
---|
| 7203 |
|
---|
| 7204 | sh2=.false.
|
---|
| 7205 | \end_layout
|
---|
| 7206 |
|
---|
| 7207 | \begin_layout Standard
|
---|
| 7208 |
|
---|
| 7209 | itysol=1
|
---|
| 7210 | \end_layout
|
---|
| 7211 |
|
---|
| 7212 | \begin_layout Standard
|
---|
| 7213 |
|
---|
| 7214 |
|
---|
| 7215 | \backslash
|
---|
| 7216 | end{verbatim}
|
---|
| 7217 | \end_layout
|
---|
| 7218 |
|
---|
| 7219 | \end_inset
|
---|
| 7220 |
|
---|
| 7221 |
|
---|
| 7222 | \end_layout
|
---|
| 7223 |
|
---|
| 7224 | \begin_layout Standard
|
---|
| 7225 | After initialization, the program calls
|
---|
| 7226 | \emph on
|
---|
| 7227 | init_molecule
|
---|
| 7228 | \emph default
|
---|
| 7229 | once for every molecule.
|
---|
| 7230 | Only the last call contains a reference to a variable file.
|
---|
| 7231 | It contains the global coordinates for each molecule
|
---|
| 7232 | \end_layout
|
---|
| 7233 |
|
---|
| 7234 | \begin_layout Standard
|
---|
| 7235 | \begin_inset ERT
|
---|
| 7236 | status open
|
---|
| 7237 |
|
---|
| 7238 | \begin_layout Standard
|
---|
| 7239 |
|
---|
| 7240 |
|
---|
| 7241 | \backslash
|
---|
| 7242 | begin{verbatim}
|
---|
| 7243 | \end_layout
|
---|
| 7244 |
|
---|
| 7245 | \begin_layout Standard
|
---|
| 7246 |
|
---|
| 7247 | @ 1 : 100, 100, 100, 0, 0, 0
|
---|
| 7248 | \end_layout
|
---|
| 7249 |
|
---|
| 7250 | \begin_layout Standard
|
---|
| 7251 |
|
---|
| 7252 | @ 2 : -100, -100, -100, 0, 0, 0
|
---|
| 7253 | \end_layout
|
---|
| 7254 |
|
---|
| 7255 | \begin_layout Standard
|
---|
| 7256 |
|
---|
| 7257 | @ 3 : 100, -100, 100, 0, 0, 0
|
---|
| 7258 | \end_layout
|
---|
| 7259 |
|
---|
| 7260 | \begin_layout Standard
|
---|
| 7261 |
|
---|
| 7262 | @ 4 : 100, -100, -100, 0, 0, 0
|
---|
| 7263 | \end_layout
|
---|
| 7264 |
|
---|
| 7265 | \begin_layout Standard
|
---|
| 7266 |
|
---|
| 7267 |
|
---|
| 7268 | \backslash
|
---|
| 7269 | end{verbatim}
|
---|
| 7270 | \end_layout
|
---|
| 7271 |
|
---|
| 7272 | \end_inset
|
---|
| 7273 |
|
---|
| 7274 |
|
---|
| 7275 | \end_layout
|
---|
| 7276 |
|
---|
| 7277 | \begin_layout Standard
|
---|
| 7278 | The subroutine reads the distribution of temperatures (in our example 'temperatu
|
---|
| 7279 | res_abeta') that has to be provided.
|
---|
| 7280 | \end_layout
|
---|
| 7281 |
|
---|
| 7282 | \begin_layout Standard
|
---|
| 7283 | The simulation starts from a stretched configuration with 100 sweeps for
|
---|
| 7284 | equilibration.
|
---|
| 7285 | The molecule is then studied over 10,000 sweeps on each node, with measurements
|
---|
| 7286 | taken every 10 sweep.
|
---|
| 7287 |
|
---|
| 7288 | \end_layout
|
---|
| 7289 |
|
---|
| 7290 | \begin_layout Standard
|
---|
| 7291 | Hence the following arguments have to be passed
|
---|
| 7292 | \end_layout
|
---|
| 7293 |
|
---|
| 7294 | \begin_layout Standard
|
---|
| 7295 | \begin_inset ERT
|
---|
| 7296 | status open
|
---|
| 7297 |
|
---|
| 7298 | \begin_layout Standard
|
---|
| 7299 |
|
---|
| 7300 |
|
---|
| 7301 | \backslash
|
---|
| 7302 | begin{verbatim}
|
---|
| 7303 | \end_layout
|
---|
| 7304 |
|
---|
| 7305 | \begin_layout Standard
|
---|
| 7306 |
|
---|
| 7307 | nequi=100
|
---|
| 7308 | \end_layout
|
---|
| 7309 |
|
---|
| 7310 | \begin_layout Standard
|
---|
| 7311 |
|
---|
| 7312 | nswp=10000
|
---|
| 7313 | \end_layout
|
---|
| 7314 |
|
---|
| 7315 | \begin_layout Standard
|
---|
| 7316 |
|
---|
| 7317 | nmes=10
|
---|
| 7318 | \end_layout
|
---|
| 7319 |
|
---|
| 7320 | \begin_layout Standard
|
---|
| 7321 |
|
---|
| 7322 | nsave=1000
|
---|
| 7323 | \end_layout
|
---|
| 7324 |
|
---|
| 7325 | \begin_layout Standard
|
---|
| 7326 |
|
---|
| 7327 | switch=0
|
---|
| 7328 | \end_layout
|
---|
| 7329 |
|
---|
| 7330 | \begin_layout Standard
|
---|
| 7331 |
|
---|
| 7332 | newsta=.true.
|
---|
| 7333 | \end_layout
|
---|
| 7334 |
|
---|
| 7335 | \begin_layout Standard
|
---|
| 7336 |
|
---|
| 7337 |
|
---|
| 7338 | \backslash
|
---|
| 7339 | end{verbatim}
|
---|
| 7340 | \end_layout
|
---|
| 7341 |
|
---|
| 7342 | \end_inset
|
---|
| 7343 |
|
---|
| 7344 | by calling
|
---|
| 7345 | \emph on
|
---|
| 7346 | partem_p(num_replica, nequi, nswp, nmes, nsave, newsta, switch, rep_id,
|
---|
| 7347 | partem_comm).
|
---|
| 7348 | \end_layout
|
---|
| 7349 |
|
---|
| 7350 | \begin_layout Standard
|
---|
| 7351 | After compiling with
|
---|
| 7352 | \emph on
|
---|
| 7353 | make parallel_tempering
|
---|
| 7354 | \emph default
|
---|
| 7355 | the program is ready to run.
|
---|
| 7356 | Note that you must first execute
|
---|
| 7357 | \emph on
|
---|
| 7358 | make parallel
|
---|
| 7359 | \emph default
|
---|
| 7360 | in the top-level directory.
|
---|
| 7361 | We do not provide a script to launch the program since launching it depends
|
---|
| 7362 | on the specific MPI installation.
|
---|
| 7363 | The data are written into the file '
|
---|
| 7364 | \shape italic
|
---|
| 7365 | ts.d
|
---|
| 7366 | \shape default
|
---|
| 7367 | '.
|
---|
| 7368 | In our case, the data are the sweep, the temperature index, the index of
|
---|
| 7369 | the replica this temperature is currently associated, the inverse temperature,
|
---|
| 7370 | and energy, radius-of gyration, number of residues that are part of a helix
|
---|
| 7371 | or sheet, number of hydrogen bond, total number of contacts and the number
|
---|
| 7372 | of contacts that appear also in the reference configuration:
|
---|
| 7373 | \begin_inset ERT
|
---|
| 7374 | status open
|
---|
| 7375 |
|
---|
| 7376 | \begin_layout Standard
|
---|
| 7377 |
|
---|
| 7378 |
|
---|
| 7379 | \backslash
|
---|
| 7380 | begin{verbatim}
|
---|
| 7381 | \end_layout
|
---|
| 7382 |
|
---|
| 7383 | \begin_layout Standard
|
---|
| 7384 |
|
---|
| 7385 | 10 1 1 0.503086435280445
|
---|
| 7386 | \end_layout
|
---|
| 7387 |
|
---|
| 7388 | \begin_layout Standard
|
---|
| 7389 |
|
---|
| 7390 | 18.5259057594418 -101.020909189261 1.668390368424223E-004
|
---|
| 7391 | \end_layout
|
---|
| 7392 |
|
---|
| 7393 | \begin_layout Standard
|
---|
| 7394 |
|
---|
| 7395 | 153.870626474863 3 4 0
|
---|
| 7396 | \end_layout
|
---|
| 7397 |
|
---|
| 7398 | \begin_layout Standard
|
---|
| 7399 |
|
---|
| 7400 | 10 2 2 0.838477392134076
|
---|
| 7401 | \end_layout
|
---|
| 7402 |
|
---|
| 7403 | \begin_layout Standard
|
---|
| 7404 |
|
---|
| 7405 | -21.8597428563679 -112.839132565408 4.398819716124160E-005
|
---|
| 7406 | \end_layout
|
---|
| 7407 |
|
---|
| 7408 | \begin_layout Standard
|
---|
| 7409 |
|
---|
| 7410 | 164.067677362049 0 12 0
|
---|
| 7411 | \end_layout
|
---|
| 7412 |
|
---|
| 7413 | \begin_layout Standard
|
---|
| 7414 |
|
---|
| 7415 | 10 3 3 1.25771608820111
|
---|
| 7416 | \end_layout
|
---|
| 7417 |
|
---|
| 7418 | \begin_layout Standard
|
---|
| 7419 |
|
---|
| 7420 | -63.6878966409724 -115.697268416431 7.324283587028595E-005
|
---|
| 7421 | \end_layout
|
---|
| 7422 |
|
---|
| 7423 | \begin_layout Standard
|
---|
| 7424 |
|
---|
| 7425 | 162.383801785309 2 9 0
|
---|
| 7426 | \end_layout
|
---|
| 7427 |
|
---|
| 7428 | \begin_layout Standard
|
---|
| 7429 |
|
---|
| 7430 | 10 4 4 1.43738981508699
|
---|
| 7431 | \end_layout
|
---|
| 7432 |
|
---|
| 7433 | \begin_layout Standard
|
---|
| 7434 |
|
---|
| 7435 | -82.2329362395502 -118.850435462771 -2.589501558808733E-005
|
---|
| 7436 | \end_layout
|
---|
| 7437 |
|
---|
| 7438 | \begin_layout Standard
|
---|
| 7439 |
|
---|
| 7440 | 155.367430914339 3 8 0
|
---|
| 7441 | \end_layout
|
---|
| 7442 |
|
---|
| 7443 | \begin_layout Standard
|
---|
| 7444 |
|
---|
| 7445 | 10 5 5 1.67695478426815
|
---|
| 7446 | \end_layout
|
---|
| 7447 |
|
---|
| 7448 | \begin_layout Standard
|
---|
| 7449 |
|
---|
| 7450 | -89.8268073782128 -115.511880821486 -1.910806982598894E-004
|
---|
| 7451 | \end_layout
|
---|
| 7452 |
|
---|
| 7453 | \begin_layout Standard
|
---|
| 7454 |
|
---|
| 7455 | 156.197401324212 1 13 0
|
---|
| 7456 | \end_layout
|
---|
| 7457 |
|
---|
| 7458 | \begin_layout Standard
|
---|
| 7459 |
|
---|
| 7460 | 10 6 6 1.82940521920162
|
---|
| 7461 | \end_layout
|
---|
| 7462 |
|
---|
| 7463 | \begin_layout Standard
|
---|
| 7464 |
|
---|
| 7465 | -102.200054103571 -119.664523580541 -2.902461830424936E-005
|
---|
| 7466 | \end_layout
|
---|
| 7467 |
|
---|
| 7468 | \begin_layout Standard
|
---|
| 7469 |
|
---|
| 7470 | 158.377278261187 1 7 0
|
---|
| 7471 | \end_layout
|
---|
| 7472 |
|
---|
| 7473 | \begin_layout Standard
|
---|
| 7474 |
|
---|
| 7475 | 10 7 7 1.92017723389483
|
---|
| 7476 | \end_layout
|
---|
| 7477 |
|
---|
| 7478 | \begin_layout Standard
|
---|
| 7479 |
|
---|
| 7480 | -92.5898004594444 -111.866857243732 8.412738265616228E-005
|
---|
| 7481 | \end_layout
|
---|
| 7482 |
|
---|
| 7483 | \begin_layout Standard
|
---|
| 7484 |
|
---|
| 7485 | 156.691206902137 2 13 0
|
---|
| 7486 | \end_layout
|
---|
| 7487 |
|
---|
| 7488 | \begin_layout Standard
|
---|
| 7489 |
|
---|
| 7490 | 10 8 8 2.01234574112178
|
---|
| 7491 | \end_layout
|
---|
| 7492 |
|
---|
| 7493 | \begin_layout Standard
|
---|
| 7494 |
|
---|
| 7495 | -91.7374330640579 -118.481236403476 -1.450348059239640E-004
|
---|
| 7496 | \end_layout
|
---|
| 7497 |
|
---|
| 7498 | \begin_layout Standard
|
---|
| 7499 |
|
---|
| 7500 | 160.611273802438 0 9 0
|
---|
| 7501 | \end_layout
|
---|
| 7502 |
|
---|
| 7503 | \begin_layout Standard
|
---|
| 7504 |
|
---|
| 7505 | ...
|
---|
| 7506 | \end_layout
|
---|
| 7507 |
|
---|
| 7508 | \begin_layout Standard
|
---|
| 7509 |
|
---|
| 7510 | ...
|
---|
| 7511 | \end_layout
|
---|
| 7512 |
|
---|
| 7513 | \begin_layout Standard
|
---|
| 7514 |
|
---|
| 7515 | ...
|
---|
| 7516 | \end_layout
|
---|
| 7517 |
|
---|
| 7518 | \begin_layout Standard
|
---|
| 7519 |
|
---|
| 7520 | 10000 1 2 0.503086435280445
|
---|
| 7521 | \end_layout
|
---|
| 7522 |
|
---|
| 7523 | \begin_layout Standard
|
---|
| 7524 |
|
---|
| 7525 | 25.7121801637793 -112.113204586669 -7.981375910951304E-005
|
---|
| 7526 | \end_layout
|
---|
| 7527 |
|
---|
| 7528 | \begin_layout Standard
|
---|
| 7529 |
|
---|
| 7530 | 171.130731978089 0 5 0
|
---|
| 7531 | \end_layout
|
---|
| 7532 |
|
---|
| 7533 | \begin_layout Standard
|
---|
| 7534 |
|
---|
| 7535 | 10000 2 4 0.838477392134076
|
---|
| 7536 | \end_layout
|
---|
| 7537 |
|
---|
| 7538 | \begin_layout Standard
|
---|
| 7539 |
|
---|
| 7540 | -83.1513580270155 -119.884471326212 -3.185178277838820E-005
|
---|
| 7541 | \end_layout
|
---|
| 7542 |
|
---|
| 7543 | \begin_layout Standard
|
---|
| 7544 |
|
---|
| 7545 | 179.222034577900 4 5 0
|
---|
| 7546 | \end_layout
|
---|
| 7547 |
|
---|
| 7548 | \begin_layout Standard
|
---|
| 7549 |
|
---|
| 7550 | 10000 3 3 1.25771608820111
|
---|
| 7551 | \end_layout
|
---|
| 7552 |
|
---|
| 7553 | \begin_layout Standard
|
---|
| 7554 |
|
---|
| 7555 | -88.7115772801244 -109.660390359632 2.816222447889407E-005
|
---|
| 7556 | \end_layout
|
---|
| 7557 |
|
---|
| 7558 | \begin_layout Standard
|
---|
| 7559 |
|
---|
| 7560 | 169.412616033656 6 2 0
|
---|
| 7561 | \end_layout
|
---|
| 7562 |
|
---|
| 7563 | \begin_layout Standard
|
---|
| 7564 |
|
---|
| 7565 | 10000 4 1 1.43738981508699
|
---|
| 7566 | \end_layout
|
---|
| 7567 |
|
---|
| 7568 | \begin_layout Standard
|
---|
| 7569 |
|
---|
| 7570 | -117.230892149812 -118.180458392844 -1.362571932424056E-004
|
---|
| 7571 | \end_layout
|
---|
| 7572 |
|
---|
| 7573 | \begin_layout Standard
|
---|
| 7574 |
|
---|
| 7575 | 155.662046672612 9 3 0
|
---|
| 7576 | \end_layout
|
---|
| 7577 |
|
---|
| 7578 | \begin_layout Standard
|
---|
| 7579 |
|
---|
| 7580 | 10000 5 5 1.67695478426815
|
---|
| 7581 | \end_layout
|
---|
| 7582 |
|
---|
| 7583 | \begin_layout Standard
|
---|
| 7584 |
|
---|
| 7585 | -117.452066538358 -114.923193931984 9.292455852280616E-005
|
---|
| 7586 | \end_layout
|
---|
| 7587 |
|
---|
| 7588 | \begin_layout Standard
|
---|
| 7589 |
|
---|
| 7590 | 165.838174859018 8 4 0
|
---|
| 7591 | \end_layout
|
---|
| 7592 |
|
---|
| 7593 | \begin_layout Standard
|
---|
| 7594 |
|
---|
| 7595 | 10000 6 8 1.82940521920162
|
---|
| 7596 | \end_layout
|
---|
| 7597 |
|
---|
| 7598 | \begin_layout Standard
|
---|
| 7599 |
|
---|
| 7600 | -114.553279087787 -116.322737335011 1.354655604376923E-005
|
---|
| 7601 | \end_layout
|
---|
| 7602 |
|
---|
| 7603 | \begin_layout Standard
|
---|
| 7604 |
|
---|
| 7605 | 161.094515087733 4 4 0
|
---|
| 7606 | \end_layout
|
---|
| 7607 |
|
---|
| 7608 | \begin_layout Standard
|
---|
| 7609 |
|
---|
| 7610 | 10000 7 7 1.92017723389483
|
---|
| 7611 | \end_layout
|
---|
| 7612 |
|
---|
| 7613 | \begin_layout Standard
|
---|
| 7614 |
|
---|
| 7615 | -128.613090309274 -113.083234658370 6.618583172642824E-005
|
---|
| 7616 | \end_layout
|
---|
| 7617 |
|
---|
| 7618 | \begin_layout Standard
|
---|
| 7619 |
|
---|
| 7620 | 169.226190038938 10 0 0
|
---|
| 7621 | \end_layout
|
---|
| 7622 |
|
---|
| 7623 | \begin_layout Standard
|
---|
| 7624 |
|
---|
| 7625 | 10000 8 6 2.01234574112178
|
---|
| 7626 | \end_layout
|
---|
| 7627 |
|
---|
| 7628 | \begin_layout Standard
|
---|
| 7629 |
|
---|
| 7630 | -116.001290834057 -115.250965599594 8.095072332381373E-005
|
---|
| 7631 | \end_layout
|
---|
| 7632 |
|
---|
| 7633 | \begin_layout Standard
|
---|
| 7634 |
|
---|
| 7635 | 169.725277983610 8 4 0
|
---|
| 7636 | \end_layout
|
---|
| 7637 |
|
---|
| 7638 | \begin_layout Standard
|
---|
| 7639 |
|
---|
| 7640 | \end_layout
|
---|
| 7641 |
|
---|
| 7642 | \begin_layout Standard
|
---|
| 7643 |
|
---|
| 7644 |
|
---|
| 7645 | \backslash
|
---|
| 7646 | end{verbatim}
|
---|
| 7647 | \end_layout
|
---|
| 7648 |
|
---|
| 7649 | \end_inset
|
---|
| 7650 |
|
---|
| 7651 |
|
---|
| 7652 | \end_layout
|
---|
| 7653 |
|
---|
| 7654 | \begin_layout Standard
|
---|
| 7655 | At the end of the simulation, the final configurations are written into
|
---|
| 7656 | external files (in our case '
|
---|
| 7657 | \shape italic
|
---|
| 7658 | conf_00??
|
---|
| 7659 | \shape default
|
---|
| 7660 | ' where '??' marks the replica index.
|
---|
| 7661 | Further information for re-starts are written into '
|
---|
| 7662 | \shape italic
|
---|
| 7663 | par_R.in
|
---|
| 7664 | \shape default
|
---|
| 7665 | ' that also collects statistics on the run.
|
---|
| 7666 |
|
---|
| 7667 | \end_layout
|
---|
| 7668 |
|
---|
| 7669 | \begin_layout Subsection
|
---|
| 7670 | Parallel tempering on a serial machine.
|
---|
| 7671 | \begin_inset LatexCommand label
|
---|
| 7672 | name "sub:Parallel-tempering-on"
|
---|
| 7673 |
|
---|
| 7674 | \end_inset
|
---|
| 7675 |
|
---|
| 7676 |
|
---|
| 7677 | \end_layout
|
---|
| 7678 |
|
---|
| 7679 | \begin_layout Standard
|
---|
| 7680 | Parallel tempering is useful even if you have only a single processor machine
|
---|
| 7681 | available.
|
---|
| 7682 | The algorithm provides better convergence than canonical Monte Carlo and
|
---|
| 7683 | avoids the scheduling problems of simulated annealing.
|
---|
| 7684 | In this example (see
|
---|
| 7685 | \emph on
|
---|
| 7686 | parallel_tempering_s.f
|
---|
| 7687 | \emph default
|
---|
| 7688 | in the
|
---|
| 7689 | \emph on
|
---|
| 7690 | EXAMPLES
|
---|
| 7691 | \emph default
|
---|
| 7692 | sub directory), we perform a parallel tempering simulation on Met-enkaphalin
|
---|
| 7693 | using 5 replicas.
|
---|
| 7694 | Each replica runs at a different temperature.
|
---|
| 7695 | The temperatures are read in from the file
|
---|
| 7696 | \emph on
|
---|
| 7697 | temperatures
|
---|
| 7698 | \emph default
|
---|
| 7699 | .
|
---|
| 7700 | The values are
|
---|
| 7701 | \end_layout
|
---|
| 7702 |
|
---|
| 7703 | \begin_layout Standard
|
---|
| 7704 | \begin_inset ERT
|
---|
| 7705 | status open
|
---|
| 7706 |
|
---|
| 7707 | \begin_layout Standard
|
---|
| 7708 |
|
---|
| 7709 |
|
---|
| 7710 | \backslash
|
---|
| 7711 | begin{verbatim}
|
---|
| 7712 | \end_layout
|
---|
| 7713 |
|
---|
| 7714 | \begin_layout Standard
|
---|
| 7715 |
|
---|
| 7716 | 1 1000
|
---|
| 7717 | \end_layout
|
---|
| 7718 |
|
---|
| 7719 | \begin_layout Standard
|
---|
| 7720 |
|
---|
| 7721 | 2 600
|
---|
| 7722 | \end_layout
|
---|
| 7723 |
|
---|
| 7724 | \begin_layout Standard
|
---|
| 7725 |
|
---|
| 7726 | 3 400
|
---|
| 7727 | \end_layout
|
---|
| 7728 |
|
---|
| 7729 | \begin_layout Standard
|
---|
| 7730 |
|
---|
| 7731 | 4 300
|
---|
| 7732 | \end_layout
|
---|
| 7733 |
|
---|
| 7734 | \begin_layout Standard
|
---|
| 7735 |
|
---|
| 7736 | 5 250.
|
---|
| 7737 | \end_layout
|
---|
| 7738 |
|
---|
| 7739 | \begin_layout Standard
|
---|
| 7740 |
|
---|
| 7741 |
|
---|
| 7742 | \backslash
|
---|
| 7743 | end{verbatim}
|
---|
| 7744 | \end_layout
|
---|
| 7745 |
|
---|
| 7746 | \end_inset
|
---|
| 7747 |
|
---|
| 7748 | We start the simulation from randomized configurations with 100 sweeps
|
---|
| 7749 | for equilibration before we exchange any replicas.
|
---|
| 7750 | The main simulation takes 10,000 sweeps with measurements taken every 10
|
---|
| 7751 | sweeps.
|
---|
| 7752 | An exchange of replicas is also attempted every 10 sweeps.
|
---|
| 7753 | This gives us the following variables
|
---|
| 7754 | \end_layout
|
---|
| 7755 |
|
---|
| 7756 | \begin_layout Standard
|
---|
| 7757 | \begin_inset ERT
|
---|
| 7758 | status open
|
---|
| 7759 |
|
---|
| 7760 | \begin_layout Standard
|
---|
| 7761 |
|
---|
| 7762 |
|
---|
| 7763 | \backslash
|
---|
| 7764 | begin{verbatim}
|
---|
| 7765 | \end_layout
|
---|
| 7766 |
|
---|
| 7767 | \begin_layout Standard
|
---|
| 7768 |
|
---|
| 7769 | num_rep = 5
|
---|
| 7770 | \end_layout
|
---|
| 7771 |
|
---|
| 7772 | \begin_layout Standard
|
---|
| 7773 |
|
---|
| 7774 | nequi = 100
|
---|
| 7775 | \end_layout
|
---|
| 7776 |
|
---|
| 7777 | \begin_layout Standard
|
---|
| 7778 |
|
---|
| 7779 | nsweep = 10000
|
---|
| 7780 | \end_layout
|
---|
| 7781 |
|
---|
| 7782 | \begin_layout Standard
|
---|
| 7783 |
|
---|
| 7784 | nmes = 1
|
---|
| 7785 | \end_layout
|
---|
| 7786 |
|
---|
| 7787 | \begin_layout Standard
|
---|
| 7788 |
|
---|
| 7789 | newsta = .true.
|
---|
| 7790 |
|
---|
| 7791 | \end_layout
|
---|
| 7792 |
|
---|
| 7793 | \begin_layout Standard
|
---|
| 7794 |
|
---|
| 7795 | switch = 1
|
---|
| 7796 | \end_layout
|
---|
| 7797 |
|
---|
| 7798 | \begin_layout Standard
|
---|
| 7799 |
|
---|
| 7800 |
|
---|
| 7801 | \backslash
|
---|
| 7802 | end{verbatim}
|
---|
| 7803 | \end_layout
|
---|
| 7804 |
|
---|
| 7805 | \end_inset
|
---|
| 7806 |
|
---|
| 7807 | and we call the simulation with
|
---|
| 7808 | \begin_inset listings
|
---|
| 7809 | lstparams "breaklines=true,float=h,language=Fortran,showstringspaces=false"
|
---|
| 7810 | inline false
|
---|
| 7811 | status collapsed
|
---|
| 7812 |
|
---|
| 7813 | \begin_layout Standard
|
---|
| 7814 |
|
---|
| 7815 | call partem_s(num_rep, nequi, nsweep, nmes, nmes, newsta, switch)
|
---|
| 7816 | \end_layout
|
---|
| 7817 |
|
---|
| 7818 | \end_inset
|
---|
| 7819 |
|
---|
| 7820 | The data is written into file
|
---|
| 7821 | \emph on
|
---|
| 7822 | time.d
|
---|
| 7823 | \emph default
|
---|
| 7824 | .
|
---|
| 7825 | The final configurations are stored in
|
---|
| 7826 | \emph on
|
---|
| 7827 | conf_000?.var
|
---|
| 7828 | \emph default
|
---|
| 7829 | , where the question mark is replaced by the replica ID.
|
---|
| 7830 | \end_layout
|
---|
| 7831 |
|
---|
| 7832 | \begin_layout Standard
|
---|
| 7833 | \begin_inset LatexCommand bibtex
|
---|
| 7834 | options "unsrt"
|
---|
| 7835 | bibfiles "/home/meinke/research/writeups/bibliography"
|
---|
| 7836 |
|
---|
| 7837 | \end_inset
|
---|
| 7838 |
|
---|
| 7839 |
|
---|
| 7840 | \end_layout
|
---|
| 7841 |
|
---|
| 7842 | \begin_layout Standard
|
---|
| 7843 | \begin_inset LatexCommand printindex
|
---|
| 7844 |
|
---|
| 7845 | \end_inset
|
---|
| 7846 |
|
---|
| 7847 |
|
---|
| 7848 | \end_layout
|
---|
| 7849 |
|
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| 7850 | \end_body
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| 7851 | \end_document
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