| 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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