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