| 1 | ! ****************************************************************
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| 2 | ! Trial version implementing the semi-local conformational update
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| 3 | ! BGS (Biased Gaussian Steps). This file presently contains the
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| 4 | ! functions initlund, bgsposs and bgs.
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| 5 | !
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| 6 | ! Copyright 2007 Frank Eisenmenger, U.H.E. Hansmann,
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| 7 | ! Jan H. Meinke, Sandipan Mohanty
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| 8 | ! ****************************************************************
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| 9 |
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| 10 |
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| 11 | ! Checks if it is possible to perform a BGS update starting at the
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| 12 | ! variable indexed ipos. Calls: none.
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| 13 | logical function bgsposs(ips)
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| 14 | include 'INCL.H'
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| 15 | include 'incl_lund.h'
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| 16 | logical ians
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| 17 |
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| 18 | jv=idvr(ips)
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| 19 | iaa=nursvr(jv)
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| 20 | ians=.true.
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| 21 | ! print *,'evaluating bgs possibility for ',ips,nmvr(jv)
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| 22 | if (nmvr(jv).ne.'phi') then
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| 23 | ! print *,'bgs not possible because variable name is ',nmvr(jv)
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| 24 | ians=.false.
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| 25 | else if (iaa.gt.(irsml2(mlvr(jv))-3)) then
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| 26 | ! print *,'bgs impossible, residue too close to end'
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| 27 | ! print *,'iaa = ',iaa,' end = ',irsml2(mlvr(jv))
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| 28 | ians=.false.
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| 29 | else
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| 30 | nnonfx=0
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| 31 | do i=iaa,iaa+3
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| 32 | if (iphi(i).gt.0) then
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| 33 | if (.not.fxvr(iphi(i))) then
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| 34 | nnonfx=nnonfx+1
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| 35 | endif
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| 36 | endif
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| 37 | if (.not.fxvr(ipsi(i))) then
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| 38 | nnonfx=nnonfx+1
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| 39 | endif
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| 40 | enddo
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| 41 | if (nnonfx.lt.6) then
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| 42 | ! print *,iaa,'bgs impossible because ndof = ',nnonfx
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| 43 | ians=.false.
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| 44 | endif
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| 45 | endif
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| 46 | if (ians) then
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| 47 | ! print *,'bgs is possible for angle ',ips,jv,nmvr(jv)
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| 48 | endif
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| 49 | bgsposs=ians
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| 50 | return
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| 51 | end
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| 52 |
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| 53 | ! Biased Gaussian Steps. Implements a semi-local conformational update
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| 54 | ! which modifies the protein backbone locally in a certain range of
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| 55 | ! amino acids. The 'down-stream' parts of the molecule outside the
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| 56 | ! region of update get small rigid body translations and rotations.
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| 57 | !
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| 58 | ! Use the update sparingly. It is rather local, and is not of great
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| 59 | ! value if we need big changes in the conformation. It is recommended
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| 60 | ! that this update be used to refine a structure around a low energy
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| 61 | ! candidate structure. Even at low energies, if you always
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| 62 | ! perform BGS, the chances of coming out of that minimum are small.
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| 63 | ! So, there is a probability bgsprob, which decides whether BGS or the
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| 64 | ! normal single angle update is used.
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| 65 | !
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| 66 | ! Calls: energy, dummy (function provided as argument), addang, (rand)
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| 67 | !
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| 68 |
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| 69 | integer function bgs(eol1,dummy)
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| 70 | include 'INCL.H'
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| 71 | include 'incl_lund.h'
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| 72 | external dummy
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| 73 | dimension xiv(8,3),bv(8,3),rv(3,3),dv(3,8,3)
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| 74 | dimension ab(8), A(8,8),p(8),ppsi(8)
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| 75 | double precision ovr(mxvr)
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| 76 | ! Initialize
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| 77 | ! print *,'using BGS on angle ',nmvr(idvr(ivar))
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| 78 | if (bgsnvar.eq.0) then
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| 79 | bgs=0
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| 80 | goto 171
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| 81 | endif
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| 82 | ivar=1+grnd()*bgsnvar
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| 83 | do i=1,8
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| 84 | iph(i)=-50000
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| 85 | dph(i)=0
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| 86 | enddo
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| 87 | nph=0
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| 88 | jv=idvr(ivar)
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| 89 | ia=nursvr(jv)
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| 90 | ! Get BGS matrices based on coordinates of atoms in 4 amino acids
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| 91 | do i=1,4
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| 92 | icurraa=ia+i-1
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| 93 | if (iphi(icurraa).gt.0.and..not.fxvr(iphi(icurraa))) then
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| 94 | nph=nph+1
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| 95 | xiv(nph,1)=xat(iCa(icurraa))
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| 96 | xiv(nph,2)=yat(iCa(icurraa))
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| 97 | xiv(nph,3)=zat(iCa(icurraa))
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| 98 | bv(nph,1)=xiv(nph,1)-xat(iN(icurraa))
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| 99 | bv(nph,2)=xiv(nph,2)-yat(iN(icurraa))
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| 100 | bv(nph,3)=xiv(nph,3)-zat(iN(icurraa))
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| 101 | ab(nph)=bv(nph,1)*bv(nph,1)+bv(nph,2)*bv(nph,2)
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| 102 | & +bv(nph,3)*bv(nph,3)
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| 103 | iph(nph)=iphi(icurraa)
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| 104 | endif
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| 105 | if (.not.fxvr(ipsi(icurraa))) then
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| 106 | nph=nph+1
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| 107 | xiv(nph,1)=xat(iC(icurraa))
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| 108 | xiv(nph,2)=yat(iC(icurraa))
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| 109 | xiv(nph,3)=zat(iC(icurraa))
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| 110 | bv(nph,1)=xiv(nph,1)-xat(iCa(icurraa))
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| 111 | bv(nph,2)=xiv(nph,2)-yat(iCa(icurraa))
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| 112 | bv(nph,3)=xiv(nph,3)-zat(iCa(icurraa))
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| 113 | ab(nph)=bv(nph,1)*bv(nph,1)+bv(nph,2)*bv(nph,2)
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| 114 | & +bv(nph,3)*bv(nph,3)
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| 115 | iph(nph)=ipsi(icurraa)
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| 116 | endif
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| 117 | enddo
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| 118 | rv(1,1)=xat(iCa(ia+3))
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| 119 | rv(1,2)=yat(iCa(ia+3))
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| 120 | rv(1,3)=zat(iCa(ia+3))
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| 121 | rv(2,1)=xat(iC(ia+3))
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| 122 | rv(2,2)=yat(iC(ia+3))
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| 123 | rv(2,3)=zat(iC(ia+3))
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| 124 | rv(3,1)=xat(iC(ia+3)+1)
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| 125 | rv(3,2)=yat(iC(ia+3)+1)
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| 126 | rv(3,3)=zat(iC(ia+3)+1)
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| 127 |
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| 128 | do i=1,3
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| 129 | do j=1,nph
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| 130 | dv(i,j,1)=(1.0/ab(j))*(bv(j,2)*(rv(i,3)-xiv(j,3))-
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| 131 | & bv(j,3)*(rv(i,2)-xiv(j,2)))
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| 132 | dv(i,j,2)=(-1.0/ab(j))*(bv(j,1)*(rv(i,3)-xiv(j,3))-
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| 133 | & bv(j,3)*(rv(i,1)-xiv(j,1)))
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| 134 | dv(i,j,3)=(1.0/ab(j))*(bv(j,1)*(rv(i,2)-xiv(j,2))-
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| 135 | & bv(j,2)*(rv(i,1)-xiv(j,1)))
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| 136 | enddo
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| 137 | enddo
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| 138 | do i=1,nph
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| 139 | do j=i,nph
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| 140 | A(i,j)=0
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| 141 | do k=1,3
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| 142 | do l=1,3
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| 143 | A(i,j)=A(i,j)+dv(k,i,l)*(dv(k,j,l))
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| 144 | enddo
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| 145 | enddo
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| 146 | A(i,j)=bbgs*A(i,j)
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| 147 | if (i.eq.j) then
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| 148 | A(i,j)=A(i,j)+1
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| 149 | endif
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| 150 | A(i,j)=0.5*abgs*A(i,j)
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| 151 | enddo
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| 152 | enddo
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| 153 | do i=1,nph
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| 154 | do j=i,nph
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| 155 | sum=A(i,j)
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| 156 | do k=i-1,1,-1
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| 157 | sum=sum-A(i,k)*A(j,k)
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| 158 | enddo
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| 159 | if (i.eq.j) then
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| 160 | p(i)=sqrt(sum)
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| 161 | else
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| 162 | A(j,i)=sum/p(i)
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| 163 | endif
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| 164 | enddo
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| 165 | enddo
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| 166 | ! Generate 8 Gaussian distributed small random angles
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| 167 | do i=1,8,2
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| 168 | r1=grnd()
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| 169 | ! In the rare event that this random number is 0, just take the next
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| 170 | if (r1.le.0) r1=grnd()
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| 171 | r1=sqrt(-log(r1))
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| 172 | r2=grnd()
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| 173 | ppsi(i)=r1*cos(pi2*r2)
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| 174 | ppsi(i+1)=r1*sin(pi2*r2)
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| 175 | enddo
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| 176 | do i=1,nph
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| 177 | dph(i)=0
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| 178 | enddo
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| 179 | ! Solve lower triangular matrix to get dphi proposals
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| 180 | do i=nph,1,-1
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| 181 | sum=ppsi(i)
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| 182 | do k=i+1,nph
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| 183 | sum=sum-A(k,i)*dph(k)
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| 184 | enddo
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| 185 | dph(i)=sum/p(i)
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| 186 | enddo
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| 187 | ! Calculate intrinsic (non-Boltzmann) weight for forward process
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| 188 | ! print *,'calculating intrinsic weight for forward process'
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| 189 | sum=0
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| 190 | do i=1,nph
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| 191 | sum=sum+ppsi(i)*ppsi(i)
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| 192 | enddo
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| 193 | wfw=exp(-sum)
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| 194 | do i=1,nph
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| 195 | wfw=wfw*p(i)
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| 196 | enddo
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| 197 |
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| 198 | ! Reconstruct chain and calculate new energy
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| 199 | ! print *,'going to assign changes to the chain'
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| 200 | ovr = vlvr
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| 201 | do i=1,nph
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| 202 | vlvr(iph(i))=addang(vlvr(iph(i)),dph(i))
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| 203 | enddo
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| 204 | enw = energy()
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| 205 | ! Calculate weight for reverse process for detail balance
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| 206 | ! print *,'proceeding to calculate weight for the reverse process'
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| 207 | nph=0
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| 208 | do i=1,4
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| 209 | icurraa=ia+i-1
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| 210 | if (iphi(icurraa).gt.0.and..not.fxvr(iphi(icurraa))) then
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| 211 | nph=nph+1
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| 212 | xiv(nph,1)=xat(iCa(icurraa))
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| 213 | xiv(nph,2)=yat(iCa(icurraa))
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| 214 | xiv(nph,3)=zat(iCa(icurraa))
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| 215 | bv(nph,1)=xiv(nph,1)-xat(iN(icurraa))
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| 216 | bv(nph,2)=xiv(nph,2)-yat(iN(icurraa))
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| 217 | bv(nph,3)=xiv(nph,3)-zat(iN(icurraa))
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| 218 | ab(nph)=bv(nph,1)*bv(nph,1)+bv(nph,2)*bv(nph,2)
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| 219 | & +bv(nph,3)*bv(nph,3)
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| 220 | iph(nph)=iphi(icurraa)
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| 221 | endif
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| 222 | if (.not.fxvr(ipsi(icurraa))) then
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| 223 | nph=nph+1
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| 224 | xiv(nph,1)=xat(iC(icurraa))
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| 225 | xiv(nph,2)=yat(iC(icurraa))
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| 226 | xiv(nph,3)=zat(iC(icurraa))
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| 227 | bv(nph,1)=xiv(nph,1)-xat(iCa(icurraa))
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| 228 | bv(nph,2)=xiv(nph,2)-yat(iCa(icurraa))
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| 229 | bv(nph,3)=xiv(nph,3)-zat(iCa(icurraa))
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| 230 | ab(nph)=bv(nph,1)*bv(nph,1)+bv(nph,2)*bv(nph,2)
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| 231 | & +bv(nph,3)*bv(nph,3)
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| 232 | iph(nph)=ipsi(icurraa)
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| 233 | endif
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| 234 | enddo
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| 235 | rv(1,1)=xat(iCa(ia+3))
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| 236 | rv(1,2)=yat(iCa(ia+3))
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| 237 | rv(1,3)=zat(iCa(ia+3))
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| 238 | rv(2,1)=xat(iC(ia+3))
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| 239 | rv(2,2)=yat(iC(ia+3))
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| 240 | rv(2,3)=zat(iC(ia+3))
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| 241 | rv(3,1)=xat(iC(ia+3)+1)
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| 242 | rv(3,2)=yat(iC(ia+3)+1)
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| 243 | rv(3,3)=zat(iC(ia+3)+1)
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| 244 |
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| 245 | do i=1,3
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| 246 | do j=1,nph
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| 247 | dv(i,j,1)=(1.0/ab(j))*(bv(j,2)*(rv(i,3)-xiv(j,3))-
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| 248 | & bv(j,3)*(rv(i,2)-xiv(j,2)))
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| 249 | dv(i,j,2)=(-1.0/ab(j))*(bv(j,1)*(rv(i,3)-xiv(j,3))-
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| 250 | & bv(j,3)*(rv(i,1)-xiv(j,1)))
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| 251 | dv(i,j,3)=(1.0/ab(j))*(bv(j,1)*(rv(i,2)-xiv(j,2))-
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| 252 | & bv(j,2)*(rv(i,1)-xiv(j,1)))
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| 253 | enddo
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| 254 | enddo
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| 255 | do i=1,nph
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| 256 | do j=i,nph
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| 257 | A(i,j)=0
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| 258 | do k=1,3
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| 259 | do l=1,3
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| 260 | A(i,j)=A(i,j)+dv(k,i,l)*(dv(k,j,l))
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| 261 | enddo
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| 262 | enddo
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| 263 | A(i,j)=bbgs*A(i,j)
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| 264 | if (i.eq.j) then
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| 265 | A(i,j)=A(i,j)+1
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| 266 | endif
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| 267 | A(i,j)=0.5*abgs*A(i,j)
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| 268 | enddo
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| 269 | enddo
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| 270 | do i=1,nph
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| 271 | do j=i,nph
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| 272 | sum=A(i,j)
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| 273 | do k=i-1,1,-1
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| 274 | sum=sum-A(i,k)*A(j,k)
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| 275 | enddo
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| 276 | if (i.eq.j) then
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| 277 | p(i)=sqrt(sum)
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| 278 | else
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| 279 | A(j,i)=sum/p(i)
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| 280 | endif
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| 281 | enddo
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| 282 | enddo
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| 283 | do i=1,nph
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| 284 | ppsi(i)=p(i)*dph(i)
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| 285 | do j=i+1,nph
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| 286 | ppsi(i)=ppsi(i)+A(j,i)*dph(j)
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| 287 | enddo
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| 288 | enddo
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| 289 | sum=0
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| 290 | do i=1,nph
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| 291 | sum=sum+ppsi(i)*ppsi(i)
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| 292 | enddo
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| 293 | wbw=exp(-sum)
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| 294 | do i=1,nph
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| 295 | wbw=wbw*p(i)
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| 296 | enddo
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| 297 | ! Acceptance condition (includes additional weight)
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| 298 | rd=grnd()
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| 299 | ! print *,'generated selection random number ',rd
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| 300 | ! print *,'wfw/wbw = ',wfw/wbw
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| 301 | rd=-log(rd*wfw/wbw)
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| 302 | ! print *,'modified rd = ',rd
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| 303 | ! print *,'before calculating energy change'
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| 304 | delta = dummy(enw)-dummy(eol1)
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| 305 | ! print *,'delta = ',delta
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| 306 | ! call outpdb(0,'after.pdb')
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| 307 | ! print *,'after outpdb for after.pdb'
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| 308 | ! do i=1,nph
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| 309 | ! print *,'BGS>',i,iph(i),vlvr(iph(i)),dph(i)
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| 310 | ! enddo
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| 311 | if (rd.ge.delta) then
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| 312 | ! accept
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| 313 | eol1=enw
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| 314 | bgs=1
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| 315 | ! print *,'BGS move accepted'
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| 316 | else
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| 317 | ! reject
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| 318 | vlvr = ovr
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| 319 | ! enw=energy()
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| 320 | ! if (abs(enw-eol1).gt.0.000001) then
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| 321 | ! write(*,*) 'rejected bgs move: energy change :',eol1,enw
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| 322 | ! endif
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| 323 | ! write(*,*) 'rejected bgs move: ',eol1,enw,wfw,wbw,rd
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| 324 | bgs=0
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| 325 | endif
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| 326 | 171 continue
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| 327 | return
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| 328 | end
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| 329 |
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