X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fsrc_MD-M-newcorr%2Fq_measure1.F;fp=source%2Funres%2Fsrc_MD-M-newcorr%2Fq_measure1.F;h=9c1546d37415288577aed3f1e12c490acea8fc0d;hb=d101c97dea752458d76055fdbae49c26fff03c1f;hp=0000000000000000000000000000000000000000;hpb=325eda160c9ad2982501e091ca40606a29043712;p=unres.git diff --git a/source/unres/src_MD-M-newcorr/q_measure1.F b/source/unres/src_MD-M-newcorr/q_measure1.F new file mode 100644 index 0000000..9c1546d --- /dev/null +++ b/source/unres/src_MD-M-newcorr/q_measure1.F @@ -0,0 +1,470 @@ + 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