1 | ! **************************************************************
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2 | !
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3 | ! This file contains the subroutines: enyshe
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4 | !
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5 | ! Copyright 2003-2005 Frank Eisenmenger, U.H.E. Hansmann,
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6 | ! Shura Hayryan, Chin-Ku
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7 | ! Copyright 2007 Frank Eisenmenger, U.H.E. Hansmann,
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8 | ! Jan H. Meinke, Sandipan Mohanty
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9 | !
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10 | ! **************************************************************
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11 |
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12 | !> PURPOSE: Calculate internal energy of molecule 'nml' with ECEPP parameters
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13 | !!
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14 | !! CALLS: none
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15 | !!
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16 | !! The function loops over all moving sets within the molecule. Within
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17 | !! this loop it loops over the van-der-Waals domains of each atom in the
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18 | !! moving set and finally over the atoms that belong to the 1-4 interaction
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19 | !! set.
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20 | !< ............................................................................
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21 |
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22 | real*8 function enyshe(nml)
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23 |
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24 |
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25 | include 'INCL.H'
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26 |
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27 | ! If nml == 0 calculate the interaction between all pairs.
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28 | double precision e0, vr, cqi, xi, yi, zi, xij, yij, zij, rij2
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29 | double precision rij4, rij6, rij, sr, ep
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30 |
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31 | integer nml, ntlvr, ifivr, i1s, io, iv, ia, it, ic, i2s, ims, i1
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32 | integer i2, i, ity, ivw, j, jty, i14
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33 |
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34 | if (nml.eq.0) then
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35 | ntlvr = nvr
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36 | else
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37 | ntlvr=nvrml(nml)
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38 | endif
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39 |
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40 | if (ntlvr.eq.0) then
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41 | write (logString, '(a,i4)')
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42 | & ' enyshe> No variables defined in molecule #',nml
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43 | return
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44 | endif
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45 |
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46 | enyshe=0.0
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47 | eyel=0.0
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48 | eyvw=0.0
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49 | eyhb=0.0
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50 | eyvr=0.0
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51 | if (nml.eq.0) then
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52 | ifivr = ivrml1(1)
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53 | i1s = imsml1(ntlml) + nmsml(ntlml)
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54 | else
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55 | ! Index of first variable in molecule.
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56 | ifivr=ivrml1(nml)
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57 | ! Index of last moving set in molecule
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58 | i1s=imsml1(nml)+nmsml(nml)
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59 | endif
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60 | ! Loop over moving sets/variables in reverse order
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61 | do io=ifivr+ntlvr-1,ifivr,-1
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62 | ! The array iorvr contains the variables in an "apropriate" order.
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63 | iv=iorvr(io)
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64 | ! Index of the primary moving atom for the variable with index iv
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65 | ia=iatvr(iv)
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66 | ! Get the type of variable iv (valence length, valence angle, dihedral angle)
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67 | it=ityvr(iv)
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68 | ! Class of variable iv's potential (Q: What are they)
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69 | ic=iclvr(iv)
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70 | ! If iv is a dihedral angle ...
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71 | if (it.eq.3) then
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72 | ! Barrier height * 1/2 of the potential of iv.
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73 | e0=e0to(ic)
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74 | ! Calculate the periodic potential term. sgto is the sign of the barrier, rnto is
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75 | ! the periodicity and toat is torsion angle(?) associate with atom ia.
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76 | if (e0.ne.0.)
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77 | & eyvr=eyvr+e0*(1.0+sgto(ic)*cos(toat(ia)*rnto(ic)))
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78 | ! else if iv is a valence angle ...
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79 | elseif (it.eq.2) then
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80 | ! vr is the valence angle of ia
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81 | vr=baat(ia)
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82 | ! else if iv is a valence length...
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83 | elseif (it.eq.1) then
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84 | ! vr is the length of the valence bond
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85 | vr=blat(ia)
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86 | endif
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87 |
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88 | ! ============================================ Energies & Atomic forces
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89 | ! index of next to last moving set
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90 | i2s=i1s-1
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91 | ! index of first moving set associated with iv
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92 | i1s=imsvr1(iv)
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93 | ! Loop over all moving sets starting from the one associated with vr to the end.
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94 | do ims=i1s,i2s
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95 | ! First atom of the current moving set
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96 | i1=latms1(ims)
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97 | ! Last atom of the current moving set
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98 | i2=latms2(ims)
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99 | ! Loop over all atoms of the current moving set.
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100 | do i=i1,i2
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101 | ! Atom class of current atom
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102 | ity=ityat(i)
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103 | ! Point charge at current atom
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104 | cqi=conv*cgat(i)
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105 | ! Cartesian coordinates of current atom
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106 | xi=xat(i)
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107 | yi=yat(i)
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108 | zi=zat(i)
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109 | ! Loop over the atoms of the van der Waals domain belonging to atom i
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110 | do ivw=ivwat1(i),ivwat2(i)
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111 | ! Loop over the atoms of the van der Waals domain of the atoms of the
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112 | ! van der Waals domain of atom i
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113 | ! Q: Which atoms are in these domains?
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114 | do j=lvwat1(ivw),lvwat2(ivw)
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115 | ! Atom type of partner
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116 | jty=ityat(j)
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117 | ! Differences in cartesian coordinates
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118 | xij=xat(j)-xi
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119 | yij=yat(j)-yi
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120 | zij=zat(j)-zi
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121 | ! Cartesian distance and higher powers
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122 | rij2=xij*xij+yij*yij+zij*zij
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123 | rij4=rij2*rij2
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124 | rij6=rij4*rij2
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125 | rij=sqrt(rij2)
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126 | ! Are we using a distance dependent dielectric constant?
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127 | if(epsd) then
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128 | sr=slp*rij
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129 | ep=plt-(sr*sr+2.0*sr+2.0)*(plt-1.0)*exp(-sr)/2.0
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130 | else
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131 | ep = 1.0d0
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132 | end if
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133 | ! Coulomb interaction
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134 | eyel=eyel+cqi*cgat(j)/(rij*ep)
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135 | ! If the two atoms cannot form a hydrogen bond use 6-12 Lennard-Jones potential
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136 | if (ihbty(ity,jty).eq.0) then
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137 | eyvw=eyvw+aij(ity,jty)/(rij6*rij6)
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138 | & -cij(ity,jty)/rij6
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139 | else
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140 | ! For hydrogen bonding use 10-12 Lennard-Jones potential
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141 | eyhb=eyhb+ahb(ity,jty)/(rij6*rij6)
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142 | & -chb(ity,jty)/(rij6*rij4)
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143 | endif
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144 |
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145 | enddo
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146 | enddo
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147 |
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148 | ! Loop over 1-4 interaction partners
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149 | ! The interactions between atoms that are three bonds apart in the protein are
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150 | ! dominated by quantum mechanical effects. They are treated separately.
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151 | do i14=i14at1(i),i14at2(i)
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152 | j=l14at(i14)
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153 |
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154 | jty=ityat(j)
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155 |
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156 | xij=xat(j)-xi
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157 | yij=yat(j)-yi
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158 | zij=zat(j)-zi
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159 | rij2=xij*xij+yij*yij+zij*zij
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160 | rij4=rij2*rij2
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161 | rij6=rij4*rij2
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162 | rij = sqrt(rij2)
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163 | ! Are we using a distance dependent dielectric constant?
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164 | if(epsd) then
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165 | sr=slp*rij
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166 | ep=plt-(sr*sr+2.0*sr+2.0)*(plt-1.0)*exp(-sr)/2.0
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167 | else
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168 | ep=1.0d0
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169 | end if
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170 |
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171 | eyel=eyel+cqi*cgat(j)/(rij*ep)
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172 | ! If hydrogen bonding is not possible use 6-12 Lennard-Jones potential.
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173 | if (ihbty(ity,jty).eq.0) then
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174 | eyvw=eyvw+a14(ity,jty)/(rij6*rij6)
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175 | & -cij(ity,jty)/rij6
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176 | else
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177 | ! Use 10-12 Lennard-Jones potential for hydrogen bonds.
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178 | eyhb=eyhb+ahb(ity,jty)/(rij6*rij6)
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179 | & -chb(ity,jty)/(rij6*rij4)
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180 | endif
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181 |
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182 | enddo ! ... 1-4-partners of i
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183 |
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184 | enddo ! ... atoms i
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185 | enddo ! ... m.s.
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186 |
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187 | enddo ! ... variables
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188 |
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189 | eysm = eyel + eyvw + eyhb + eyvr
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190 |
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191 | enyshe=eysm
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192 | return
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193 | end
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194 |
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