[bd2278d] | 1 | ! **************************************************************
|
---|
| 2 | !
|
---|
[32289cd] | 3 | ! This file contains the subroutines: enyshe
|
---|
[bd2278d] | 4 | !
|
---|
| 5 | ! Copyright 2003-2005 Frank Eisenmenger, U.H.E. Hansmann,
|
---|
[32289cd] | 6 | ! Shura Hayryan, Chin-Ku
|
---|
[bd2278d] | 7 | ! Copyright 2007 Frank Eisenmenger, U.H.E. Hansmann,
|
---|
| 8 | ! Jan H. Meinke, Sandipan Mohanty
|
---|
| 9 | !
|
---|
| 10 | ! **************************************************************
|
---|
[e40e335] | 11 |
|
---|
| 12 |
|
---|
| 13 | real*8 function enyshe(nml)
|
---|
| 14 |
|
---|
[bd2278d] | 15 | ! ............................................................................
|
---|
| 16 | !
|
---|
| 17 | ! PURPOSE: Calculate internal energy of molecule 'nml' with ECEPP parameters
|
---|
| 18 | !
|
---|
| 19 | ! CALLS: none
|
---|
| 20 | !
|
---|
| 21 | ! The function loops over all moving sets within the molecule. Within
|
---|
[32289cd] | 22 | ! this loop it loops over the van-der-Waals domains of each atom in the
|
---|
[bd2278d] | 23 | ! moving set and finally over the atoms that belong to the 1-4 interaction
|
---|
| 24 | ! set.
|
---|
| 25 | ! ............................................................................
|
---|
[e40e335] | 26 |
|
---|
| 27 | include 'INCL.H'
|
---|
| 28 |
|
---|
[bd2278d] | 29 | ! If nml == 0 calculate the interaction between all pairs.
|
---|
[32289cd] | 30 | double precision e0, vr, cqi, xi, yi, zi, xij, yij, zij, rij2
|
---|
| 31 | double precision rij4, rij6, rij, sr, ep
|
---|
| 32 |
|
---|
| 33 | integer nml, ntlvr, ifivr, i1s, io, iv, ia, it, ic, i2s, ims, i1
|
---|
| 34 | integer i2, i, ity, ivw, j, jty, i14
|
---|
| 35 |
|
---|
[e40e335] | 36 | if (nml.eq.0) then
|
---|
| 37 | ntlvr = nvr
|
---|
| 38 | else
|
---|
| 39 | ntlvr=nvrml(nml)
|
---|
| 40 | endif
|
---|
[32289cd] | 41 |
|
---|
[e40e335] | 42 | if (ntlvr.eq.0) then
|
---|
[38d77eb] | 43 | write (logString, '(a,i4)')
|
---|
[bd2278d] | 44 | & ' enyshe> No variables defined in molecule #',nml
|
---|
[e40e335] | 45 | return
|
---|
| 46 | endif
|
---|
| 47 |
|
---|
| 48 | enyshe=0.0
|
---|
| 49 | eyel=0.0
|
---|
| 50 | eyvw=0.0
|
---|
| 51 | eyhb=0.0
|
---|
| 52 | eyvr=0.0
|
---|
| 53 | if (nml.eq.0) then
|
---|
| 54 | ifivr = ivrml1(1)
|
---|
| 55 | i1s = imsml1(ntlml) + nmsml(ntlml)
|
---|
[32289cd] | 56 | else
|
---|
[bd2278d] | 57 | ! Index of first variable in molecule.
|
---|
[e40e335] | 58 | ifivr=ivrml1(nml)
|
---|
[bd2278d] | 59 | ! Index of last moving set in molecule
|
---|
[e40e335] | 60 | i1s=imsml1(nml)+nmsml(nml)
|
---|
| 61 | endif
|
---|
[32289cd] | 62 | ! Loop over moving sets/variables in reverse order
|
---|
| 63 | do io=ifivr+ntlvr-1,ifivr,-1
|
---|
[bd2278d] | 64 | ! The array iorvr contains the variables in an "apropriate" order.
|
---|
[32289cd] | 65 | iv=iorvr(io)
|
---|
[bd2278d] | 66 | ! Index of the primary moving atom for the variable with index iv
|
---|
[32289cd] | 67 | ia=iatvr(iv)
|
---|
[bd2278d] | 68 | ! Get the type of variable iv (valence length, valence angle, dihedral angle)
|
---|
[32289cd] | 69 | it=ityvr(iv)
|
---|
[bd2278d] | 70 | ! Class of variable iv's potential (Q: What are they)
|
---|
[32289cd] | 71 | ic=iclvr(iv)
|
---|
[bd2278d] | 72 | ! If iv is a dihedral angle ...
|
---|
[32289cd] | 73 | if (it.eq.3) then
|
---|
[bd2278d] | 74 | ! Barrier height * 1/2 of the potential of iv.
|
---|
[e40e335] | 75 | e0=e0to(ic)
|
---|
[bd2278d] | 76 | ! Calculate the periodic potential term. sgto is the sign of the barrier, rnto is
|
---|
| 77 | ! the periodicity and toat is torsion angle(?) associate with atom ia.
|
---|
[32289cd] | 78 | if (e0.ne.0.)
|
---|
[bd2278d] | 79 | & eyvr=eyvr+e0*(1.0+sgto(ic)*cos(toat(ia)*rnto(ic)))
|
---|
| 80 | ! else if iv is a valence angle ...
|
---|
[32289cd] | 81 | elseif (it.eq.2) then
|
---|
[bd2278d] | 82 | ! vr is the valence angle of ia
|
---|
[e40e335] | 83 | vr=baat(ia)
|
---|
[bd2278d] | 84 | ! else if iv is a valence length...
|
---|
[32289cd] | 85 | elseif (it.eq.1) then
|
---|
[bd2278d] | 86 | ! vr is the length of the valence bond
|
---|
[e40e335] | 87 | vr=blat(ia)
|
---|
| 88 | endif
|
---|
| 89 |
|
---|
[bd2278d] | 90 | ! ============================================ Energies & Atomic forces
|
---|
| 91 | ! index of next to last moving set
|
---|
[e40e335] | 92 | i2s=i1s-1
|
---|
[bd2278d] | 93 | ! index of first moving set associated with iv
|
---|
[32289cd] | 94 | i1s=imsvr1(iv)
|
---|
[bd2278d] | 95 | ! Loop over all moving sets starting from the one associated with vr to the end.
|
---|
[32289cd] | 96 | do ims=i1s,i2s
|
---|
[bd2278d] | 97 | ! First atom of the current moving set
|
---|
[e40e335] | 98 | i1=latms1(ims)
|
---|
[bd2278d] | 99 | ! Last atom of the current moving set
|
---|
[e40e335] | 100 | i2=latms2(ims)
|
---|
[bd2278d] | 101 | ! Loop over all atoms of the current moving set.
|
---|
[32289cd] | 102 | do i=i1,i2
|
---|
[bd2278d] | 103 | ! Atom class of current atom
|
---|
[e40e335] | 104 | ity=ityat(i)
|
---|
[bd2278d] | 105 | ! Point charge at current atom
|
---|
[e40e335] | 106 | cqi=conv*cgat(i)
|
---|
[bd2278d] | 107 | ! Cartesian coordinates of current atom
|
---|
[e40e335] | 108 | xi=xat(i)
|
---|
| 109 | yi=yat(i)
|
---|
| 110 | zi=zat(i)
|
---|
[bd2278d] | 111 | ! Loop over the atoms of the van der Waals domain belonging to atom i
|
---|
[32289cd] | 112 | do ivw=ivwat1(i),ivwat2(i)
|
---|
| 113 | ! Loop over the atoms of the van der Waals domain of the atoms of the
|
---|
[bd2278d] | 114 | ! van der Waals domain of atom i
|
---|
| 115 | ! Q: Which atoms are in these domains?
|
---|
[32289cd] | 116 | do j=lvwat1(ivw),lvwat2(ivw)
|
---|
[bd2278d] | 117 | ! Atom type of partner
|
---|
[e40e335] | 118 | jty=ityat(j)
|
---|
[bd2278d] | 119 | ! Differences in cartesian coordinates
|
---|
[e40e335] | 120 | xij=xat(j)-xi
|
---|
| 121 | yij=yat(j)-yi
|
---|
| 122 | zij=zat(j)-zi
|
---|
[bd2278d] | 123 | ! Cartesian distance and higher powers
|
---|
[e40e335] | 124 | rij2=xij*xij+yij*yij+zij*zij
|
---|
| 125 | rij4=rij2*rij2
|
---|
| 126 | rij6=rij4*rij2
|
---|
| 127 | rij=sqrt(rij2)
|
---|
[bd2278d] | 128 | ! Are we using a distance dependent dielectric constant?
|
---|
[e40e335] | 129 | if(epsd) then
|
---|
| 130 | sr=slp*rij
|
---|
| 131 | ep=plt-(sr*sr+2.0*sr+2.0)*(plt-1.0)*exp(-sr)/2.0
|
---|
| 132 | else
|
---|
| 133 | ep = 1.0d0
|
---|
| 134 | end if
|
---|
[bd2278d] | 135 | ! Coulomb interaction
|
---|
[e40e335] | 136 | eyel=eyel+cqi*cgat(j)/(rij*ep)
|
---|
[bd2278d] | 137 | ! If the two atoms cannot form a hydrogen bond use 6-12 Lennard-Jones potential
|
---|
[e40e335] | 138 | if (ihbty(ity,jty).eq.0) then
|
---|
| 139 | eyvw=eyvw+aij(ity,jty)/(rij6*rij6)
|
---|
[bd2278d] | 140 | & -cij(ity,jty)/rij6
|
---|
[e40e335] | 141 | else
|
---|
[bd2278d] | 142 | ! For hydrogen bonding use 10-12 Lennard-Jones potential
|
---|
[e40e335] | 143 | eyhb=eyhb+ahb(ity,jty)/(rij6*rij6)
|
---|
[bd2278d] | 144 | & -chb(ity,jty)/(rij6*rij4)
|
---|
[e40e335] | 145 | endif
|
---|
| 146 |
|
---|
[32289cd] | 147 | enddo
|
---|
| 148 | enddo
|
---|
| 149 |
|
---|
[bd2278d] | 150 | ! Loop over 1-4 interaction partners
|
---|
| 151 | ! The interactions between atoms that are three bonds apart in the protein are
|
---|
| 152 | ! dominated by quantum mechanical effects. They are treated separately.
|
---|
[32289cd] | 153 | do i14=i14at1(i),i14at2(i)
|
---|
[e40e335] | 154 | j=l14at(i14)
|
---|
| 155 |
|
---|
| 156 | jty=ityat(j)
|
---|
| 157 |
|
---|
| 158 | xij=xat(j)-xi
|
---|
| 159 | yij=yat(j)-yi
|
---|
| 160 | zij=zat(j)-zi
|
---|
| 161 | rij2=xij*xij+yij*yij+zij*zij
|
---|
| 162 | rij4=rij2*rij2
|
---|
| 163 | rij6=rij4*rij2
|
---|
| 164 | rij = sqrt(rij2)
|
---|
[bd2278d] | 165 | ! Are we using a distance dependent dielectric constant?
|
---|
[e40e335] | 166 | if(epsd) then
|
---|
| 167 | sr=slp*rij
|
---|
| 168 | ep=plt-(sr*sr+2.0*sr+2.0)*(plt-1.0)*exp(-sr)/2.0
|
---|
| 169 | else
|
---|
| 170 | ep=1.0d0
|
---|
| 171 | end if
|
---|
| 172 |
|
---|
| 173 | eyel=eyel+cqi*cgat(j)/(rij*ep)
|
---|
[bd2278d] | 174 | ! If hydrogen bonding is not possible use 6-12 Lennard-Jones potential.
|
---|
[e40e335] | 175 | if (ihbty(ity,jty).eq.0) then
|
---|
| 176 | eyvw=eyvw+a14(ity,jty)/(rij6*rij6)
|
---|
[bd2278d] | 177 | & -cij(ity,jty)/rij6
|
---|
[e40e335] | 178 | else
|
---|
[bd2278d] | 179 | ! Use 10-12 Lennard-Jones potential for hydrogen bonds.
|
---|
[e40e335] | 180 | eyhb=eyhb+ahb(ity,jty)/(rij6*rij6)
|
---|
[bd2278d] | 181 | & -chb(ity,jty)/(rij6*rij4)
|
---|
[e40e335] | 182 | endif
|
---|
| 183 |
|
---|
| 184 | enddo ! ... 1-4-partners of i
|
---|
| 185 |
|
---|
| 186 | enddo ! ... atoms i
|
---|
| 187 | enddo ! ... m.s.
|
---|
| 188 |
|
---|
| 189 | enddo ! ... variables
|
---|
| 190 |
|
---|
| 191 | eysm = eyel + eyvw + eyhb + eyvr
|
---|
| 192 |
|
---|
| 193 | enyshe=eysm
|
---|
| 194 | return
|
---|
| 195 | end
|
---|
| 196 |
|
---|