--- /dev/null
+ double precision function qwolynes(seg1,seg2,flag,seg3,seg4)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.INTERACT'
+ include 'COMMON.VAR'
+ include 'COMMON.MD'
+ integer i,j,jl,k,l,il,kl,nl,np,seg1,seg2,seg3,seg4,secseg
+ integer nsep /3/
+ double precision dist,qm
+ double precision qq,qqij,qqijCM,dij,d0ij,dijCM,d0ijCM
+ logical lprn /.false./
+ logical flag
+ qq = 0.0d0
+ nl=0
+ do i=0,nres
+ do j=1,3
+ dqwol(j,i)=0.0d0
+ dxqwol(j,i)=0.0d0
+ enddo
+ enddo
+ if (lprn) then
+ write (iout,*) "seg1",seg1," seg2",seg2," seg3",seg3," seg4",seg4,
+ & " flag",flag
+ call flush(iout)
+ endif
+ if (flag) then
+ do il=seg1+nsep,seg2
+ do jl=seg1,il-nsep
+ nl=nl+1
+ if (itype(il).ne.10) then
+ ilnres=il+nres
+ else
+ ilnres=il
+ endif
+ if (itype(jl).ne.10) then
+ jlnres=jl+nres
+ else
+ jlnres=jl
+ endif
+ qqijCM = qcontrib(il,jl,ilnres,jlnres)
+ qq = qq+qqijCM
+ if (lprn) then
+ write (iout,*) "qqijCM",qqijCM
+ call flush(iout)
+ endif
+ enddo
+ enddo
+ if (lprn) then
+ write (iout,*) "nl",nl," qq",qq
+ call flush(iout)
+ endif
+ else
+ do il=seg1,seg2
+ if((seg3-il).lt.3) then
+ secseg=il+3
+ else
+ secseg=seg3
+ endif
+ do jl=secseg,seg4
+ nl=nl+1
+ if (itype(il).ne.10) then
+ ilnres=il+nres
+ else
+ ilnres=il
+ endif
+ if (itype(jl).ne.10) then
+ jlnres=jl+nres
+ else
+ jlnres=jl
+ endif
+ qqijCM = qcontrib(il,jl,ilnres,jlnres)
+ qq = qq+qqijCM
+ if (lprn) then
+ write (iout,*) "qqijCM",qqijCM
+ call flush(iout)
+ endif
+ enddo
+ enddo
+ endif
+ qq = qq/nl
+ qwolynes=1.0d0-qq
+ do i=0,nres
+ do j=1,3
+ dqwol(j,i)=dqwol(j,i)/nl
+ dxqwol(j,i)=dxqwol(j,i)/nl
+ enddo
+ enddo
+ return
+ end
+c-------------------------------------------------------------------
+ subroutine qwol_num(seg1,seg2,flag,seg3,seg4)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.INTERACT'
+ include 'COMMON.VAR'
+ include 'COMMON.MD'
+ integer seg1,seg2,seg3,seg4
+ logical flag
+ double precision qwolan(3,0:maxres),cdummy(3,0:maxres2),
+ & qwolxan(3,0:maxres),q1,q2
+ double precision delta /1.0d-7/
+ write (iout,*) "seg1",seg1," seg2",seg2," seg3",seg3," seg4",seg4
+ write(iout,*) "dQ/dc backbone "
+ do i=0,nres
+ write(iout,'(i5,3e15.5)') i, (dqwol(j,i),j=1,3)
+ enddo
+ write(iout,*) "dQ/dX side chain "
+ do i=1,nres
+ write(iout,'(i5,3e15.5)') i,(dxqwol(j,i),j=1,3)
+ enddo
+ do i=1,nres
+ do j=1,3
+ cdummy(j,i)=c(j,i)
+ c(j,i)=c(j,i)-delta
+ q1=qwolynes(seg1,seg2,flag,seg3,seg4)
+ c(j,i)=cdummy(j,i)+delta
+ q2=qwolynes(seg1,seg2,flag,seg3,seg4)
+ qwolan(j,i)=0.5d0*(q2-q1)/delta
+ c(j,i)=cdummy(j,i)
+c write (iout,*) "i",i," j",j," q1",q1," a2",q2
+ enddo
+ enddo
+ do i=1,nres
+ do j=1,3
+ cdummy(j,i+nres)=c(j,i+nres)
+ c(j,i+nres)=c(j,i+nres)-delta
+ q1=qwolynes(seg1,seg2,flag,seg3,seg4)
+ c(j,i+nres)=cdummy(j,i+nres)+delta
+ q2=qwolynes(seg1,seg2,flag,seg3,seg4)
+ qwolxan(j,i)=0.5d0*(q2-q1)/delta
+ c(j,i+nres)=cdummy(j,i+nres)
+ enddo
+ enddo
+ write(iout,*) "Numerical Q cartesian gradients backbone: "
+ do i=0,nres
+ write(iout,'(i5,3e15.5)') i, (qwolan(j,i),j=1,3)
+ enddo
+ write(iout,*) "Numerical Q cartesian gradients side-chain: "
+ do i=0,nres
+ write(iout,'(i5,3e15.5)') i, (qwolxan(j,i),j=1,3)
+ enddo
+ return
+ end
+c------------------------------------------------------------------------
+ subroutine EconstrQ
+c MD with umbrella_sampling using Wolyne's distance measure as a constraint
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.CONTROL'
+ include 'COMMON.VAR'
+ include 'COMMON.MD'
+#ifndef LANG0
+ include 'COMMON.LANGEVIN'
+#else
+ include 'COMMON.LANGEVIN.lang0'
+#endif
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.GEO'
+ include 'COMMON.LOCAL'
+ include 'COMMON.INTERACT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.NAMES'
+ include 'COMMON.TIME1'
+ double precision uzap1,uzap2,hm1,hm2,hmnum
+ double precision ucdelan,dUcartan(3,0:MAXRES)
+ & ,dUxcartan(3,0:MAXRES),cdummy(3,0:MAXRES),
+ & duconst(3,0:MAXRES),duxconst(3,0:MAXRES)
+ integer kstart,kend,lstart,lend,idummy
+ double precision delta /1.0d-7/
+ do i=0,nres
+ do j=1,3
+ duconst(j,i)=0.0d0
+ dudconst(j,i)=0.0d0
+ duxconst(j,i)=0.0d0
+ dudxconst(j,i)=0.0d0
+ enddo
+ enddo
+ Uconst=0.0d0
+ do i=1,nfrag
+ qfrag(i)=qwolynes(ifrag(1,i,iset),ifrag(2,i,iset),.true.
+ & ,idummy,idummy)
+ Uconst=Uconst+wfrag(i,iset)*harmonic(qfrag(i),qinfrag(i,iset))
+c Calculating the derivatives of Constraint energy with respect to Q
+ Ucdfrag=wfrag(i,iset)*harmonicprim(qfrag(i),qinfrag(i,iset))
+c Calculating the derivatives of Q with respect to cartesian coordinates
+ do ii=0,nres
+ do j=1,3
+ duconst(j,ii)=dUconst(j,ii)+ucdfrag*dqwol(j,ii)
+ dUxconst(j,ii)=dUxconst(j,ii)+ucdfrag*dxqwol(j,ii)
+ enddo
+ enddo
+c write (iout,*) "Calling qwol_num"
+c call qwol_num(ifrag(1,i),ifrag(2,i),.true.,idummy,idummy)
+ enddo
+ do i=1,npair
+ kstart=ifrag(1,ipair(1,i,iset),iset)
+ kend=ifrag(2,ipair(1,i,iset),iset)
+ lstart=ifrag(1,ipair(2,i,iset),iset)
+ lend=ifrag(2,ipair(2,i,iset),iset)
+ qpair(i)=qwolynes(kstart,kend,.false.,lstart,lend)
+ Uconst=Uconst+wpair(i,iset)*harmonic(qpair(i),qinpair(i,iset))
+c Calculating dU/dQ
+ Ucdpair=wpair(i,iset)*harmonicprim(qpair(i),qinpair(i,iset))
+c Calculating dQ/dXi
+ do ii=0,nres
+ do j=1,3
+ duconst(j,ii)=dUconst(j,ii)+ucdpair*dqwol(j,ii)
+ dUxconst(j,ii)=dUxconst(j,ii)+ucdpair*dxqwol(j,ii)
+ enddo
+ enddo
+ enddo
+c write(iout,*) "Uconst inside subroutine ", Uconst
+c Transforming the gradients from Cs to dCs for the backbone
+ do i=0,nres
+ do j=i+1,nres
+ do k=1,3
+ dudconst(k,i)=dudconst(k,i)+duconst(k,j)+duxconst(k,j)
+ enddo
+ enddo
+ enddo
+c Transforming the gradients from Cs to dCs for the side chains
+ do i=1,nres
+ do j=1,3
+ dudxconst(j,i)=duxconst(j,i)
+ enddo
+ enddo
+c write(iout,*) "dU/dc backbone "
+c do ii=0,nres
+c write(iout,'(i5,3e15.5)') ii, (duconst(j,ii),j=1,3)
+c enddo
+c write(iout,*) "dU/dX side chain "
+c do ii=1,nres
+c write(iout,'(i5,3e15.5)') ii,(duxconst(j,ii),j=1,3)
+c enddo
+c write(iout,*) "dU/ddc backbone "
+c do ii=0,nres
+c write(iout,'(i5,3e15.5)') ii, (dudconst(j,ii),j=1,3)
+c enddo
+c write(iout,*) "dU/ddX side chain "
+c do ii=1,nres
+c write(iout,'(i5,3e15.5)') ii,(dudxconst(j,ii),j=1,3)
+c enddo
+c Calculating numerical gradients of dUconst/ddc and dUconst/ddx
+c call dEconstrQ_num
+ return
+ end
+c-----------------------------------------------------------------------
+ subroutine dEconstrQ_num
+c Calculating numerical dUconst/ddc and dUconst/ddx
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.CONTROL'
+ include 'COMMON.VAR'
+ include 'COMMON.MD'
+#ifndef LANG0
+ include 'COMMON.LANGEVIN'
+#else
+ include 'COMMON.LANGEVIN.lang0'
+#endif
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.GEO'
+ include 'COMMON.LOCAL'
+ include 'COMMON.INTERACT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.NAMES'
+ include 'COMMON.TIME1'
+ double precision uzap1,uzap2
+ double precision dUcartan(3,0:MAXRES)
+ & ,dUxcartan(3,0:MAXRES),cdummy(3,0:MAXRES)
+ integer kstart,kend,lstart,lend,idummy
+ double precision delta /1.0d-7/
+c For the backbone
+ do i=0,nres-1
+ do j=1,3
+ dUcartan(j,i)=0.0d0
+ cdummy(j,i)=dc(j,i)
+ dc(j,i)=dc(j,i)+delta
+ call chainbuild_cart
+ uzap2=0.0d0
+ do ii=1,nfrag
+ qfrag(ii)=qwolynes(ifrag(1,ii,iset),ifrag(2,ii,iset),
+ & .true.,idummy,idummy)
+ uzap2=uzap2+wfrag(ii,iset)*harmonic(qfrag(ii),
+ & qinfrag(ii,iset))
+ enddo
+ do ii=1,npair
+ kstart=ifrag(1,ipair(1,ii,iset),iset)
+ kend=ifrag(2,ipair(1,ii,iset),iset)
+ lstart=ifrag(1,ipair(2,ii,iset),iset)
+ lend=ifrag(2,ipair(2,ii,iset),iset)
+ qpair(ii)=qwolynes(kstart,kend,.false.,lstart,lend)
+ uzap2=uzap2+wpair(ii,iset)*
+ & harmonic(qpair(ii),qinpair(ii,iset))
+ enddo
+ dc(j,i)=cdummy(j,i)
+ call chainbuild_cart
+ uzap1=0.0d0
+ do ii=1,nfrag
+ qfrag(ii)=qwolynes(ifrag(1,ii,iset),ifrag(2,ii,iset),
+ & .true.,idummy,idummy)
+ uzap1=uzap1+wfrag(ii,iset)*
+ & harmonic(qfrag(ii),qinfrag(ii,iset))
+ enddo
+ do ii=1,npair
+ kstart=ifrag(1,ipair(1,ii,iset),iset)
+ kend=ifrag(2,ipair(1,ii,iset),iset)
+ lstart=ifrag(1,ipair(2,ii,iset),iset)
+ lend=ifrag(2,ipair(2,ii,iset),iset)
+ qpair(ii)=qwolynes(kstart,kend,.false.,lstart,lend)
+ uzap1=uzap1+wpair(ii,iset)*
+ & harmonic(qpair(ii),qinpair(ii,iset))
+ enddo
+ ducartan(j,i)=(uzap2-uzap1)/(delta)
+ enddo
+ enddo
+c Calculating numerical gradients for dU/ddx
+ do i=0,nres-1
+ do j=1,3
+ duxcartan(j,i)=0.0d0
+ enddo
+ do j=1,3
+ cdummy(j,i)=dc(j,i+nres)
+ dc(j,i+nres)=dc(j,i+nres)+delta
+ call chainbuild_cart
+ uzap2=0.0d0
+ do ii=1,nfrag
+ qfrag(ii)=qwolynes(ifrag(1,ii,iset),ifrag(2,ii,iset),
+ & .true.,idummy,idummy)
+ uzap2=uzap2+wfrag(ii,iset)*
+ & harmonic(qfrag(ii),qinfrag(ii,iset))
+ enddo
+ do ii=1,npair
+ kstart=ifrag(1,ipair(1,ii,iset),iset)
+ kend=ifrag(2,ipair(1,ii,iset),iset)
+ lstart=ifrag(1,ipair(2,ii,iset),iset)
+ lend=ifrag(2,ipair(2,ii,iset),iset)
+ qpair(ii)=qwolynes(kstart,kend,.false.,lstart,lend)
+ uzap2=uzap2+wpair(ii,iset)*
+ & harmonic(qpair(ii),qinpair(ii,iset))
+ enddo
+ dc(j,i+nres)=cdummy(j,i)
+ call chainbuild_cart
+ uzap1=0.0d0
+ do ii=1,nfrag
+ qfrag(ii)=qwolynes(ifrag(1,ii,iset),ifrag(2,ii,iset),
+ & .true.,idummy,idummy)
+ uzap1=uzap1+wfrag(ii,iset)*
+ & harmonic(qfrag(ii),qinfrag(ii,iset))
+ enddo
+ do ii=1,npair
+ kstart=ifrag(1,ipair(1,ii,iset),iset)
+ kend=ifrag(2,ipair(1,ii,iset),iset)
+ lstart=ifrag(1,ipair(2,ii,iset),iset)
+ lend=ifrag(2,ipair(2,ii,iset),iset)
+ qpair(ii)=qwolynes(kstart,kend,.false.,lstart,lend)
+ uzap1=uzap1+wpair(ii,iset)*
+ & harmonic(qpair(ii),qinpair(ii,iset))
+ enddo
+ duxcartan(j,i)=(uzap2-uzap1)/(delta)
+ enddo
+ enddo
+ write(iout,*) "Numerical dUconst/ddc backbone "
+ do ii=0,nres
+ write(iout,'(i5,3e15.5)') ii,(dUcartan(j,ii),j=1,3)
+ enddo
+ write(iout,*) "Numerical dUconst/ddx side-chain "
+ do ii=1,nres
+ write(iout,'(i5,3e15.5)') ii,(dUxcartan(j,ii),j=1,3)
+ enddo
+ return
+ end
+c---------------------------------------------------------------------------
+ double precision function qcontrib(il,jl,il1,jl1)
+ implicit none
+ include 'DIMENSIONS'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.INTERACT'
+ include 'COMMON.MD'
+ integer i,j,k,il,jl,il1,jl1,nd
+ double precision dist
+ external dist
+ double precision dij1,dij2,dij3,dij4,d0ij1,d0ij2,d0ij3,d0ij4,fac,
+ & fac1,ddave,ssij,ddqij
+ logical lprn /.false./
+ d0ij1=dsqrt((cref(1,jl)-cref(1,il))**2+
+ & (cref(2,jl)-cref(2,il))**2+
+ & (cref(3,jl)-cref(3,il))**2)
+ dij1=dist(il,jl)
+ ddave=(dij1-d0ij1)**2
+ nd=1
+ if (jl1.ne.jl) then
+ d0ij2=dsqrt((cref(1,jl1)-cref(1,il))**2+
+ & (cref(2,jl1)-cref(2,il))**2+
+ & (cref(3,jl1)-cref(3,il))**2)
+ dij2=dist(il,jl1)
+ ddave=ddave+(dij2-d0ij2)**2
+ nd=nd+1
+ endif
+ if (il1.ne.il) then
+ d0ij3=dsqrt((cref(1,jl)-cref(1,il1))**2+
+ & (cref(2,jl)-cref(2,il1))**2+
+ & (cref(3,jl)-cref(3,il1))**2)
+ dij3=dist(il1,jl)
+ ddave=ddave+(dij3-d0ij3)**2
+ nd=nd+1
+ endif
+ if (il1.ne.il .and. jl1.ne.jl) then
+ d0ij4=dsqrt((cref(1,jl1)-cref(1,il1))**2+
+ & (cref(2,jl1)-cref(2,il1))**2+
+ & (cref(3,jl1)-cref(3,il1))**2)
+ dij4=dist(il1,jl1)
+ ddave=ddave+(dij4-d0ij4)**2
+ nd=nd+1
+ endif
+ ddave=ddave/nd
+ if (lprn) then
+ write (iout,*) "il",il," jl",jl,
+ & " itype",itype(il),itype(jl)," nd",nd
+ write (iout,*)"d0ij",d0ij1,d0ij2,d0ij3,d0ij4,
+ & " dij",dij1,dij2,dij3,dij4," ddave",ddave
+ call flush(iout)
+ endif
+c ssij = (0.25d0*d0ij1)**2
+ if (il.ne.il1 .and. jl.ne.jl1) then
+ ssij = 16.0d0/(d0ij1*d0ij4)
+ else
+ ssij = 16.0d0/(d0ij1*d0ij1)
+ endif
+ qcontrib = dexp(-0.5d0*ddave*ssij)
+c Compute gradient
+ fac1 = qcontrib*ssij/nd
+ fac = fac1*(dij1-d0ij1)/dij1
+ do k=1,3
+ ddqij = (c(k,il)-c(k,jl))*fac
+ dqwol(k,il)=dqwol(k,il)+ddqij
+ dqwol(k,jl)=dqwol(k,jl)-ddqij
+ enddo
+ if (jl1.ne.jl) then
+ fac = fac1*(dij2-d0ij2)/dij2
+ do k=1,3
+ ddqij = (c(k,il)-c(k,jl1))*fac
+ dqwol(k,il)=dqwol(k,il)+ddqij
+ dxqwol(k,jl)=dxqwol(k,jl)-ddqij
+ enddo
+ endif
+ if (il1.ne.il) then
+ fac = fac1*(dij3-d0ij3)/dij3
+ do k=1,3
+ ddqij = (c(k,il1)-c(k,jl))*fac
+ dxqwol(k,il)=dxqwol(k,il)+ddqij
+ dqwol(k,jl)=dqwol(k,jl)-ddqij
+ enddo
+ endif
+ if (il1.ne.il .and. jl1.ne.jl) then
+ fac = fac1*(dij4-d0ij4)/dij4
+ do k=1,3
+ ddqij = (c(k,il1)-c(k,jl1))*fac
+ dxqwol(k,il)=dxqwol(k,il)+ddqij
+ dxqwol(k,jl)=dxqwol(k,jl)-ddqij
+ enddo
+ endif
+ return
+ end
projects / unres.git / blobdiff