X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fsrc_MD-NEWSC%2Fq_measure.F;fp=source%2Funres%2Fsrc_MD-NEWSC%2Fq_measure.F;h=417cf35a56488d9d4253e46990e53042b1d37d3b;hb=d101c97dea752458d76055fdbae49c26fff03c1f;hp=0000000000000000000000000000000000000000;hpb=325eda160c9ad2982501e091ca40606a29043712;p=unres.git diff --git a/source/unres/src_MD-NEWSC/q_measure.F b/source/unres/src_MD-NEWSC/q_measure.F new file mode 100644 index 0000000..417cf35 --- /dev/null +++ b/source/unres/src_MD-NEWSC/q_measure.F @@ -0,0 +1,487 @@ + 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' + integer i,j,jl,k,l,il,kl,nl,np,ip,kp,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 + double precision sigm,x + sigm(x)=0.25d0*x + qq = 0.0d0 + nl=0 + if(flag) then + do il=seg1+nsep,seg2 + do jl=seg1,il-nsep + nl=nl+1 + d0ij=dsqrt((cref(1,jl)-cref(1,il))**2+ + & (cref(2,jl)-cref(2,il))**2+ + & (cref(3,jl)-cref(3,il))**2) + dij=dist(il,jl) + qqij = dexp(-0.5d0*((dij-d0ij)/(sigm(d0ij)))**2) + if (itype(il).ne.10 .or. itype(jl).ne.10) then + nl=nl+1 + d0ijCM=dsqrt( + & (cref(1,jl+nres)-cref(1,il+nres))**2+ + & (cref(2,jl+nres)-cref(2,il+nres))**2+ + & (cref(3,jl+nres)-cref(3,il+nres))**2) + dijCM=dist(il+nres,jl+nres) + qqijCM = dexp(-0.5d0*((dijCM-d0ijCM)/(sigm(d0ijCM)))**2) + endif + qq = qq+qqij+qqijCM + enddo + enddo + qq = qq/nl + 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 + d0ij=dsqrt((cref(1,jl)-cref(1,il))**2+ + & (cref(2,jl)-cref(2,il))**2+ + & (cref(3,jl)-cref(3,il))**2) + dij=dist(il,jl) + qqij = dexp(-0.5d0*((dij-d0ij)/(sigm(d0ij)))**2) + if (itype(il).ne.10 .or. itype(jl).ne.10) then + nl=nl+1 + d0ijCM=dsqrt( + & (cref(1,jl+nres)-cref(1,il+nres))**2+ + & (cref(2,jl+nres)-cref(2,il+nres))**2+ + & (cref(3,jl+nres)-cref(3,il+nres))**2) + dijCM=dist(il+nres,jl+nres) + qqijCM = dexp(-0.5d0*((dijCM-d0ijCM)/(sigm(d0ijCM)))**2) + endif + qq = qq+qqij+qqijCM + enddo + enddo + qq = qq/nl + endif + qwolynes=1.0d0-qq + return + end +c------------------------------------------------------------------- + subroutine qwolynes_prim(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,nl,seg1,seg2,seg3,seg4, + & secseg + integer nsep /3/ + double precision dist + double precision dij,d0ij,dijCM,d0ijCM + logical lprn /.false./ + logical flag + double precision sigm,x,sim,dd0,fac,ddqij + sigm(x)=0.25d0*x + + do i=0,nres + do j=1,3 + dqwol(j,i)=0.0d0 + dxqwol(j,i)=0.0d0 + enddo + enddo + nl=0 + if(flag) then + do il=seg1+nsep,seg2 + do jl=seg1,il-nsep + nl=nl+1 + d0ij=dsqrt((cref(1,jl)-cref(1,il))**2+ + & (cref(2,jl)-cref(2,il))**2+ + & (cref(3,jl)-cref(3,il))**2) + dij=dist(il,jl) + sim = 1.0d0/sigm(d0ij) + sim = sim*sim + dd0 = dij-d0ij + fac = dd0*sim/dij*dexp(-0.5d0*dd0*dd0*sim) + 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 (itype(il).ne.10 .or. itype(jl).ne.10) then + nl=nl+1 + d0ijCM=dsqrt( + & (cref(1,jl+nres)-cref(1,il+nres))**2+ + & (cref(2,jl+nres)-cref(2,il+nres))**2+ + & (cref(3,jl+nres)-cref(3,il+nres))**2) + dijCM=dist(il+nres,jl+nres) + sim = 1.0d0/sigm(d0ijCM) + sim = sim*sim + dd0=dijCM-d0ijCM + fac=dd0*sim/dijCM*dexp(-0.5d0*dd0*dd0*sim) + do k=1,3 + ddqij = (c(k,il+nres)-c(k,jl+nres))*fac + dxqwol(k,il)=dxqwol(k,il)+ddqij + dxqwol(k,jl)=dxqwol(k,jl)-ddqij + enddo + endif + enddo + enddo + 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 + d0ij=dsqrt((cref(1,jl)-cref(1,il))**2+ + & (cref(2,jl)-cref(2,il))**2+ + & (cref(3,jl)-cref(3,il))**2) + dij=dist(il,jl) + sim = 1.0d0/sigm(d0ij) + sim = sim*sim + dd0 = dij-d0ij + fac = dd0*sim/dij*dexp(-0.5d0*dd0*dd0*sim) + 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 (itype(il).ne.10 .or. itype(jl).ne.10) then + nl=nl+1 + d0ijCM=dsqrt( + & (cref(1,jl+nres)-cref(1,il+nres))**2+ + & (cref(2,jl+nres)-cref(2,il+nres))**2+ + & (cref(3,jl+nres)-cref(3,il+nres))**2) + dijCM=dist(il+nres,jl+nres) + sim = 1.0d0/sigm(d0ijCM) + sim=sim*sim + dd0 = dijCM-d0ijCM + fac = dd0*sim/dijCM*dexp(-0.5d0*dd0*dd0*sim) + do k=1,3 + ddqij = (c(k,il+nres)-c(k,jl+nres))*fac + dxqwol(k,il)=dxqwol(k,il)+ddqij + dxqwol(k,jl)=dxqwol(k,jl)-ddqij + enddo + endif + enddo + enddo + endif + 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' + 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-10/ + do i=0,nres + do j=1,3 + q1=qwolynes(seg1,seg2,flag,seg3,seg4) + cdummy(j,i)=c(j,i) + c(j,i)=c(j,i)+delta + q2=qwolynes(seg1,seg2,flag,seg3,seg4) + qwolan(j,i)=(q2-q1)/delta + c(j,i)=cdummy(j,i) + enddo + enddo + do i=0,nres + do j=1,3 + q1=qwolynes(seg1,seg2,flag,seg3,seg4) + cdummy(j,i+nres)=c(j,i+nres) + c(j,i+nres)=c(j,i+nres)+delta + q2=qwolynes(seg1,seg2,flag,seg3,seg4) + qwolxan(j,i)=(q2-q1)/delta + c(j,i+nres)=cdummy(j,i+nres) + enddo + enddo +c write(iout,*) "Numerical Q carteisan gradients backbone: " +c do i=0,nct +c write(iout,'(i5,3e15.5)') i, (qwolan(j,i),j=1,3) +c enddo +c write(iout,*) "Numerical Q carteisan gradients side-chain: " +c do i=0,nct +c write(iout,'(i5,3e15.5)') i, (qwolxan(j,i),j=1,3) +c 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 hm1=harmonic(qfrag(i,iset),qinfrag(i,iset)) +c hm2=harmonic(qfrag(i,iset)+delta,qinfrag(i,iset)) +c hmnum=(hm2-hm1)/delta +c write(iout,*) "harmonicprim frag",harmonicprim(qfrag(i,iset), +c & qinfrag(i,iset)) +c write(iout,*) "harmonicnum frag", hmnum +c Calculating the derivatives of Q with respect to cartesian coordinates + call qwolynes_prim(ifrag(1,i,iset),ifrag(2,i,iset),.true. + & ,idummy,idummy) +c write(iout,*) "dqwol " +c do ii=1,nres +c write(iout,'(i5,3e15.5)') ii,(dqwol(j,ii),j=1,3) +c enddo +c write(iout,*) "dxqwol " +c do ii=1,nres +c write(iout,'(i5,3e15.5)') ii,(dxqwol(j,ii),j=1,3) +c enddo +c Calculating numerical gradients of dU/dQi and dQi/dxi +c call qwol_num(ifrag(1,i,iset),ifrag(2,i,iset),.true. +c & ,idummy,idummy) +c The gradients of Uconst in Cs + 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 + 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 hm1=harmonic(qpair(i),qinpair(i,iset)) +c hm2=harmonic(qpair(i)+delta,qinpair(i,iset)) +c hmnum=(hm2-hm1)/delta +c write(iout,*) "harmonicprim pair ",harmonicprim(qpair(i), +c & qinpair(i,iset)) +c write(iout,*) "harmonicnum pair ", hmnum +c Calculating dQ/dXi + call qwolynes_prim(kstart,kend,.false. + & ,lstart,lend) +c write(iout,*) "dqwol " +c do ii=1,nres +c write(iout,'(i5,3e15.5)') ii,(dqwol(j,ii),j=1,3) +c enddo +c write(iout,*) "dxqwol " +c do ii=1,nres +c write(iout,'(i5,3e15.5)') ii,(dxqwol(j,ii),j=1,3) +c enddo +c Calculating numerical gradients +c call qwol_num(kstart,kend,.false. +c & ,lstart,lend) +c The gradients of Uconst in Cs + 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/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,(duxconst(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 + duxcartan(j,i)=0.0d0 + 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 +c write(iout,*) "Numerical dUconst/ddx side-chain " +c do ii=1,nres +c write(iout,'(i5,3e15.5)') ii,(dUxcartan(j,ii),j=1,3) +c enddo + return + end +c---------------------------------------------------------------------------