From: Adam Sieradzan Date: Wed, 17 Dec 2014 09:40:58 +0000 (+0100) Subject: Merge branch 'master' of mmka:unres into multichain X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=commitdiff_plain;h=9b46e3da575cb549a4070ee7d0c75efc729951e6;hp=-c;p=unres.git Merge branch 'master' of mmka:unres into multichain Conflicts: .gitignore bin/cluster/unres_clustMD-mult_MPICH-GAB.exe bin/unres/MD/unres_gfortran_single_GAB.exe bin/unres/MD/unres_ifort_single_GAB.exe bin/unres/MINIM/unres_ifort_MIN_single_E0LL2Y.exe bin/unres/MINIM/unres_ifort_MIN_single_GAB.exe bin/unres_clustMD_MPI-oldparm bin/wham/wham_multparm-ham_rep-oldparm source/cluster/wham/src/COMMON.SCCOR source/cluster/wham/src/Makefile source/unres/src_MD-M/MREMD.F source/unres/src_MD-M/Makefile source/unres/src_MD-M/energy_p_new_barrier.F source/unres/src_MD-M/stochfric.F source/unres/src_MD-M/unres.F source/unres/src_MD/cinfo.f source/wham/src-M/Makefile source/wham/src/DIMENSIONS.FREE --- 9b46e3da575cb549a4070ee7d0c75efc729951e6 diff --combined CMakeLists.txt index 9b6b6b8,5b824dd..89bd8ef --- a/CMakeLists.txt +++ b/CMakeLists.txt @@@ -6,8 -6,8 +6,8 @@@ cmake_minimum_required(VERSION 2.8 project(UNRESPACK Fortran C) set(UNRES_MAJOR 3) - set(UNRES_MINOR 1) - set(UNRES_PATCH 0) + set(UNRES_MINOR 2) + set(UNRES_PATCH 1) set(UNRES_VERSION ${UNRES_MAJOR}.${UNRES_MINOR}.${UNRES_PATCH}) #====================================== @@@ -63,6 -63,13 +63,13 @@@ MACRO (CINFO_FORMAT FN VN VD file(APPEND ${FN} " write(iout,*)'${STR}'\n") endif(SUMA GREATER 50) ENDMACRO (CINFO_FORMAT) + + # Some MPI wrappers pass double include paths + # This macro fixes broken by semicolon occurence in path + MACRO (FIX_DBL_INCLUDE RESULT) + string(REPLACE ";" " -I" ${RESULT} "${${RESULT}}") + ENDMACRO (FIX_DBL_INCLUDE) + #====================================== # CTest stuff #======================================A @@@ -70,8 -77,6 +77,6 @@@ include(CTest) enable_testing() - # Set makefile verbose on - set( CMAKE_VERBOSE_MAKEFILE 1 ) #====================================== # Fortran compilers stuff @@@ -88,10 -93,23 +93,23 @@@ SET(CMAKE_Fortran_COMPILE_OBJECT ">>>>>> f5379d3246c4bd95e946c4d35d4a1c13e329c4cb call ssbond_ene(iii,jjj,eij) ehpb=ehpb+2*eij + endif cd write (iout,*) "eij",eij else C Calculate the distance between the two points and its difference from the C target distance. - dd=dist(ii,jj) - rdis=dd-dhpb(i) + dd=dist(ii,jj) + rdis=dd-dhpb(i) C Get the force constant corresponding to this distance. - waga=forcon(i) + waga=forcon(i) C Calculate the contribution to energy. - ehpb=ehpb+waga*rdis*rdis + ehpb=ehpb+waga*rdis*rdis C C Evaluate gradient. C - fac=waga*rdis/dd + fac=waga*rdis/dd cd print *,'i=',i,' ii=',ii,' jj=',jj,' dhpb=',dhpb(i),' dd=',dd, cd & ' waga=',waga,' fac=',fac - do j=1,3 - ggg(j)=fac*(c(j,jj)-c(j,ii)) - enddo + do j=1,3 + ggg(j)=fac*(c(j,jj)-c(j,ii)) + enddo cd print '(i3,3(1pe14.5))',i,(ggg(j),j=1,3) C If this is a SC-SC distance, we need to calculate the contributions to the C Cartesian gradient in the SC vectors (ghpbx). - if (iii.lt.ii) then + if (iii.lt.ii) then do j=1,3 ghpbx(j,iii)=ghpbx(j,iii)-ggg(j) ghpbx(j,jjj)=ghpbx(j,jjj)+ggg(j) enddo - endif + endif cgrad do j=iii,jjj-1 cgrad do k=1,3 cgrad ghpbc(k,j)=ghpbc(k,j)+ggg(k) cgrad enddo cgrad enddo - do k=1,3 - ghpbc(k,jjj)=ghpbc(k,jjj)+ggg(k) - ghpbc(k,iii)=ghpbc(k,iii)-ggg(k) - enddo + do k=1,3 + ghpbc(k,jjj)=ghpbc(k,jjj)+ggg(k) + ghpbc(k,iii)=ghpbc(k,iii)-ggg(k) + enddo endif enddo ehpb=0.5D0*ehpb @@@ -4700,7 -4109,7 +4722,7 @@@ include 'COMMON.VAR' include 'COMMON.IOUNITS' double precision erij(3),dcosom1(3),dcosom2(3),gg(3) - itypi=itype(i) + itypi=iabs(itype(i)) xi=c(1,nres+i) yi=c(2,nres+i) zi=c(3,nres+i) @@@ -4709,7 -4118,7 +4731,7 @@@ dzi=dc_norm(3,nres+i) c dsci_inv=dsc_inv(itypi) dsci_inv=vbld_inv(nres+i) - itypj=itype(j) + itypj=iabs(itype(j)) c dscj_inv=dsc_inv(itypj) dscj_inv=vbld_inv(nres+j) xj=c(1,nres+j)-xi @@@ -4791,43 -4200,36 +4813,43 @@@ estr=0.0d0 estr1=0.0d0 do i=ibondp_start,ibondp_end - if (itype(i-1).eq.21 .or. itype(i).eq.21) then - estr1=estr1+gnmr1(vbld(i),-1.0d0,distchainmax) - do j=1,3 - gradb(j,i-1)=gnmr1prim(vbld(i),-1.0d0,distchainmax) - & *dc(j,i-1)/vbld(i) - enddo - if (energy_dec) write(iout,*) - & "estr1",i,gnmr1(vbld(i),-1.0d0,distchainmax) - else + if (itype(i-1).eq.ntyp1 .and. itype(i).eq.ntyp1) cycle +c estr1=estr1+gnmr1(vbld(i),-1.0d0,distchainmax) +c do j=1,3 +c gradb(j,i-1)=gnmr1prim(vbld(i),-1.0d0,distchainmax) +c & *dc(j,i-1)/vbld(i) +c enddo +c if (energy_dec) write(iout,*) +c & "estr1",i,gnmr1(vbld(i),-1.0d0,distchainmax) +c else +C Checking if it involves dummy (NH3+ or COO-) group + if (itype(i-1).eq.ntyp1 .or. itype(i).eq.ntyp1) then +C YES vbldpDUM is the equlibrium length of spring for Dummy atom + diff = vbld(i)-vbldpDUM + else +C NO vbldp0 is the equlibrium lenght of spring for peptide group diff = vbld(i)-vbldp0 - if (energy_dec) write (iout,*) + endif + if (energy_dec) write (iout,'(a7,i5,4f7.3)') & "estr bb",i,vbld(i),vbldp0,diff,AKP*diff*diff estr=estr+diff*diff do j=1,3 gradb(j,i-1)=AKP*diff*dc(j,i-1)/vbld(i) enddo c write (iout,'(i5,3f10.5)') i,(gradb(j,i-1),j=1,3) - endif +c endif enddo estr=0.5d0*AKP*estr+estr1 c c 09/18/07 AL: multimodal bond potential based on AM1 CA-SC PMF's included c do i=ibond_start,ibond_end - iti=itype(i) - if (iti.ne.10 .and. iti.ne.21) then + iti=iabs(itype(i)) + if (iti.ne.10 .and. iti.ne.ntyp1) then nbi=nbondterm(iti) if (nbi.eq.1) then diff=vbld(i+nres)-vbldsc0(1,iti) - if (energy_dec) write (iout,*) + if (energy_dec) write (iout,*) & "estr sc",i,iti,vbld(i+nres),vbldsc0(1,iti),diff, & AKSC(1,iti),AKSC(1,iti)*diff*diff estr=estr+0.5d0*AKSC(1,iti)*diff*diff @@@ -4896,25 -4298,11 +4918,25 @@@ c time12=1.0d etheta=0.0D0 c write (*,'(a,i2)') 'EBEND ICG=',icg do i=ithet_start,ithet_end - if (itype(i-1).eq.21) cycle + if ((itype(i-1).eq.ntyp1).or.itype(i-2).eq.ntyp1 + & .or.itype(i).eq.ntyp1) cycle C Zero the energy function and its derivative at 0 or pi. call splinthet(theta(i),0.5d0*delta,ss,ssd) it=itype(i-1) - if (i.gt.3 .and. itype(i-2).ne.21) then + ichir1=isign(1,itype(i-2)) + ichir2=isign(1,itype(i)) + if (itype(i-2).eq.10) ichir1=isign(1,itype(i-1)) + if (itype(i).eq.10) ichir2=isign(1,itype(i-1)) + if (itype(i-1).eq.10) then + itype1=isign(10,itype(i-2)) + ichir11=isign(1,itype(i-2)) + ichir12=isign(1,itype(i-2)) + itype2=isign(10,itype(i)) + ichir21=isign(1,itype(i)) + ichir22=isign(1,itype(i)) + endif + + if (i.gt.3 .and. itype(i-3).ne.ntyp1) then #ifdef OSF phii=phi(i) if (phii.ne.phii) phii=150.0 @@@ -4927,7 -4315,7 +4949,7 @@@ y(1)=0.0D0 y(2)=0.0D0 endif - if (i.lt.nres .and. itype(i).ne.21) then + if (i.lt.nres .and. itype(i+1).ne.ntyp1) then #ifdef OSF phii1=phi(i+1) if (phii1.ne.phii1) phii1=150.0 @@@ -4935,8 -4323,8 +4957,8 @@@ z(1)=cos(phii1) #else phii1=phi(i+1) - z(1)=dcos(phii1) #endif + z(1)=dcos(phii1) z(2)=dsin(phii1) else z(1)=0.0D0 @@@ -4947,28 -4335,15 +4969,28 @@@ C dependent on the adjacent virtual-bon C In following comments this theta will be referred to as t_c. thet_pred_mean=0.0d0 do k=1,2 - athetk=athet(k,it) - bthetk=bthet(k,it) - thet_pred_mean=thet_pred_mean+athetk*y(k)+bthetk*z(k) + athetk=athet(k,it,ichir1,ichir2) + bthetk=bthet(k,it,ichir1,ichir2) + if (it.eq.10) then + athetk=athet(k,itype1,ichir11,ichir12) + bthetk=bthet(k,itype2,ichir21,ichir22) + endif + thet_pred_mean=thet_pred_mean+athetk*y(k)+bthetk*z(k) +c write(iout,*) 'chuj tu', y(k),z(k) enddo dthett=thet_pred_mean*ssd thet_pred_mean=thet_pred_mean*ss+a0thet(it) C Derivatives of the "mean" values in gamma1 and gamma2. - dthetg1=(-athet(1,it)*y(2)+athet(2,it)*y(1))*ss - dthetg2=(-bthet(1,it)*z(2)+bthet(2,it)*z(1))*ss + dthetg1=(-athet(1,it,ichir1,ichir2)*y(2) + &+athet(2,it,ichir1,ichir2)*y(1))*ss + dthetg2=(-bthet(1,it,ichir1,ichir2)*z(2) + & +bthet(2,it,ichir1,ichir2)*z(1))*ss + if (it.eq.10) then + dthetg1=(-athet(1,itype1,ichir11,ichir12)*y(2) + &+athet(2,itype1,ichir11,ichir12)*y(1))*ss + dthetg2=(-bthet(1,itype2,ichir21,ichir22)*z(2) + & +bthet(2,itype2,ichir21,ichir22)*z(1))*ss + endif if (theta(i).gt.pi-delta) then call theteng(pi-delta,thet_pred_mean,theta0(it),f0,fprim0, & E_tc0) @@@ -4991,11 -4366,11 +5013,11 @@@ & E_theta,E_tc) endif etheta=etheta+ethetai - if (energy_dec) write (iout,'(a6,i5,0pf7.3)') - & 'ebend',i,ethetai + if (energy_dec) write (iout,'(a6,i5,0pf7.3,f7.3,i5)') + & 'ebend',i,ethetai,theta(i),itype(i) if (i.gt.3) gloc(i-3,icg)=gloc(i-3,icg)+wang*E_tc*dthetg1 if (i.lt.nres) gloc(i-2,icg)=gloc(i-2,icg)+wang*E_tc*dthetg2 - gloc(nphi+i-2,icg)=wang*(E_theta+E_tc*dthett) + gloc(nphi+i-2,icg)=wang*(E_theta+E_tc*dthett)+gloc(nphi+i-2,icg) enddo C Ufff.... We've done all this!!! return @@@ -5013,8 -4388,7 +5035,8 @@@ C-------------------------------------- C Calculate the contributions to both Gaussian lobes. C 6/6/97 - Deform the Gaussians using the factor of 1/(1+time) C The "polynomial part" of the "standard deviation" of this part of -C the distribution. +C the distributioni. +ccc write (iout,*) thetai,thet_pred_mean sig=polthet(3,it) do j=2,0,-1 sig=sig*thet_pred_mean+polthet(j,it) @@@ -5044,7 -4418,6 +5066,7 @@@ C Following variable is sigma(t_c)**(-2 delthe0=thetai-theta0i term1=-0.5D0*sigcsq*delthec*delthec term2=-0.5D0*sig0inv*delthe0*delthe0 +C write (iout,*)'term1',term1,term2,sigcsq,delthec,sig0inv,delthe0 C Following fuzzy logic is to avoid underflows in dexp and subsequent INFs and C NaNs in taking the logarithm. We extract the largest exponent which is added C to the energy (this being the log of the distribution) at the end of energy @@@ -5072,7 -4445,6 +5094,7 @@@ C Contribution of the bending energy fr C the sum of the contributions from the two lobes and the pre-exponential C factor. Simple enough, isn't it? ethetai=(-dlog(termexp)-termm+dlog(termpre)) +C write (iout,*) 'termexp',termexp,termm,termpre,i C NOW the derivatives!!! C 6/6/97 Take into account the deformation. E_theta=(delthec*sigcsq*term1 @@@ -5139,31 -4511,24 +5161,31 @@@ logical lprn /.false./, lprn1 /.false./ etheta=0.0D0 do i=ithet_start,ithet_end - if (itype(i-1).eq.21) cycle +c print *,i,itype(i-1),itype(i),itype(i-2) + if ((itype(i-1).eq.ntyp1).or.itype(i-2).eq.ntyp1 + & .or.itype(i).eq.ntyp1) cycle +C In current verion the ALL DUMMY ATOM POTENTIALS ARE OFF + + if (iabs(itype(i+1)).eq.20) iblock=2 + if (iabs(itype(i+1)).ne.20) iblock=1 dethetai=0.0d0 dephii=0.0d0 dephii1=0.0d0 theti2=0.5d0*theta(i) - ityp2=ithetyp(itype(i-1)) + ityp2=ithetyp((itype(i-1))) do k=1,nntheterm coskt(k)=dcos(k*theti2) sinkt(k)=dsin(k*theti2) enddo - if (i.gt.3 .and. itype(i-2).ne.21) then + if (i.gt.3 .and. itype(i-3).ne.ntyp1) then #ifdef OSF phii=phi(i) if (phii.ne.phii) phii=150.0 #else phii=phi(i) #endif - ityp1=ithetyp(itype(i-2)) + ityp1=ithetyp((itype(i-2))) +C propagation of chirality for glycine type do k=1,nsingle cosph1(k)=dcos(k*phii) sinph1(k)=dsin(k*phii) @@@ -5176,7 -4541,7 +5198,7 @@@ sinph1(k)=0.0d0 enddo endif - if (i.lt.nres .and. itype(i).ne.21) then + if (i.lt.nres .and. itype(i+1).ne.ntyp1) then #ifdef OSF phii1=phi(i+1) if (phii1.ne.phii1) phii1=150.0 @@@ -5184,7 -4549,7 +5206,7 @@@ #else phii1=phi(i+1) #endif - ityp3=ithetyp(itype(i)) + ityp3=ithetyp((itype(i))) do k=1,nsingle cosph2(k)=dcos(k*phii1) sinph2(k)=dsin(k*phii1) @@@ -5197,7 -4562,7 +5219,7 @@@ sinph2(k)=0.0d0 enddo endif - ethetai=aa0thet(ityp1,ityp2,ityp3) + ethetai=aa0thet(ityp1,ityp2,ityp3,iblock) do k=1,ndouble do l=1,k-1 ccl=cosph1(l)*cosph2(k-l) @@@ -5219,12 -4584,11 +5241,12 @@@ enddo endif do k=1,ntheterm - ethetai=ethetai+aathet(k,ityp1,ityp2,ityp3)*sinkt(k) - dethetai=dethetai+0.5d0*k*aathet(k,ityp1,ityp2,ityp3) + ethetai=ethetai+aathet(k,ityp1,ityp2,ityp3,iblock)*sinkt(k) + dethetai=dethetai+0.5d0*k*aathet(k,ityp1,ityp2,ityp3,iblock) & *coskt(k) if (lprn) - & write (iout,*) "k",k," aathet",aathet(k,ityp1,ityp2,ityp3), + & write (iout,*) "k",k," + & aathet",aathet(k,ityp1,ityp2,ityp3,iblock), & " ethetai",ethetai enddo if (lprn) then @@@ -5243,24 -4607,24 +5265,24 @@@ endif do m=1,ntheterm2 do k=1,nsingle - aux=bbthet(k,m,ityp1,ityp2,ityp3)*cosph1(k) - & +ccthet(k,m,ityp1,ityp2,ityp3)*sinph1(k) - & +ddthet(k,m,ityp1,ityp2,ityp3)*cosph2(k) - & +eethet(k,m,ityp1,ityp2,ityp3)*sinph2(k) + aux=bbthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph1(k) + & +ccthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph1(k) + & +ddthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph2(k) + & +eethet(k,m,ityp1,ityp2,ityp3,iblock)*sinph2(k) ethetai=ethetai+sinkt(m)*aux dethetai=dethetai+0.5d0*m*aux*coskt(m) dephii=dephii+k*sinkt(m)*( - & ccthet(k,m,ityp1,ityp2,ityp3)*cosph1(k)- - & bbthet(k,m,ityp1,ityp2,ityp3)*sinph1(k)) + & ccthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph1(k)- + & bbthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph1(k)) dephii1=dephii1+k*sinkt(m)*( - & eethet(k,m,ityp1,ityp2,ityp3)*cosph2(k)- - & ddthet(k,m,ityp1,ityp2,ityp3)*sinph2(k)) + & eethet(k,m,ityp1,ityp2,ityp3,iblock)*cosph2(k)- + & ddthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph2(k)) if (lprn) & write (iout,*) "m",m," k",k," bbthet", - & bbthet(k,m,ityp1,ityp2,ityp3)," ccthet", - & ccthet(k,m,ityp1,ityp2,ityp3)," ddthet", - & ddthet(k,m,ityp1,ityp2,ityp3)," eethet", - & eethet(k,m,ityp1,ityp2,ityp3)," ethetai",ethetai + & bbthet(k,m,ityp1,ityp2,ityp3,iblock)," ccthet", + & ccthet(k,m,ityp1,ityp2,ityp3,iblock)," ddthet", + & ddthet(k,m,ityp1,ityp2,ityp3,iblock)," eethet", + & eethet(k,m,ityp1,ityp2,ityp3,iblock)," ethetai",ethetai enddo enddo if (lprn) @@@ -5268,29 -4632,28 +5290,29 @@@ do m=1,ntheterm3 do k=2,ndouble do l=1,k-1 - aux=ffthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)+ - & ffthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l)+ - & ggthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)+ - & ggthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l) + aux=ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)+ + & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l)+ + & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)+ + & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l) ethetai=ethetai+sinkt(m)*aux dethetai=dethetai+0.5d0*m*coskt(m)*aux dephii=dephii+l*sinkt(m)*( - & -ffthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)- - & ffthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)+ - & ggthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)+ - & ggthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l)) + & -ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)- + & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l)+ + & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)+ + & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l)) dephii1=dephii1+(k-l)*sinkt(m)*( - & -ffthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)+ - & ffthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)+ - & ggthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)- - & ggthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l)) + & -ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)+ + & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l)+ + & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)- + & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l)) if (lprn) then write (iout,*) "m",m," k",k," l",l," ffthet", - & ffthet(l,k,m,ityp1,ityp2,ityp3), - & ffthet(k,l,m,ityp1,ityp2,ityp3)," ggthet", - & ggthet(l,k,m,ityp1,ityp2,ityp3), - & ggthet(k,l,m,ityp1,ityp2,ityp3)," ethetai",ethetai + & ffthet(l,k,m,ityp1,ityp2,ityp3,iblock), + & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)," ggthet", + & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock), + & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock), + & " ethetai",ethetai write (iout,*) cosph1ph2(l,k)*sinkt(m), & cosph1ph2(k,l)*sinkt(m), & sinph1ph2(l,k)*sinkt(m),sinph1ph2(k,l)*sinkt(m) @@@ -5299,16 -4662,13 +5321,16 @@@ enddo enddo 10 continue - if (lprn1) write (iout,'(i2,3f8.1,9h ethetai ,f10.5)') +c lprn1=.true. + if (lprn1) + & write (iout,'(i2,3f8.1,9h ethetai ,f10.5)') & i,theta(i)*rad2deg,phii*rad2deg, & phii1*rad2deg,ethetai +c lprn1=.false. etheta=etheta+ethetai if (i.gt.3) gloc(i-3,icg)=gloc(i-3,icg)+wang*dephii if (i.lt.nres) gloc(i-2,icg)=gloc(i-2,icg)+wang*dephii1 - gloc(nphi+i-2,icg)=wang*dethetai + gloc(nphi+i-2,icg)=wang*dethetai+ gloc(nphi+i-2,icg) enddo return end @@@ -5339,9 -4699,9 +5361,9 @@@ C ALPHA and OMEGA c write (iout,'(a)') 'ESC' do i=loc_start,loc_end it=itype(i) - if (it.eq.21) cycle + if (it.eq.ntyp1) cycle if (it.eq.10) goto 1 - nlobit=nlob(it) + nlobit=nlob(iabs(it)) c print *,'i=',i,' it=',it,' nlobit=',nlobit c write (iout,*) 'i=',i,' ssa=',ssa,' ssad=',ssad theti=theta(i+1)-pipol @@@ -5498,11 -4858,11 +5520,11 @@@ C Compute the contribution to SC energ do j=1,nlobit #ifdef OSF - adexp=bsc(j,it)-0.5D0*contr(j,iii)+emin + adexp=bsc(j,iabs(it))-0.5D0*contr(j,iii)+emin if(adexp.ne.adexp) adexp=1.0 expfac=dexp(adexp) #else - expfac=dexp(bsc(j,it)-0.5D0*contr(j,iii)+emin) + expfac=dexp(bsc(j,iabs(it))-0.5D0*contr(j,iii)+emin) #endif cd print *,'j=',j,' expfac=',expfac escloc_i=escloc_i+expfac @@@ -5584,7 -4944,7 +5606,7 @@@ C Compute the contribution to SC energ dersc12=0.0d0 do j=1,nlobit - expfac=dexp(bsc(j,it)-0.5D0*contr(j)+emin) + expfac=dexp(bsc(j,iabs(it))-0.5D0*contr(j)+emin) escloc_i=escloc_i+expfac do k=1,2 dersc(k)=dersc(k)+Ax(k,j)*expfac @@@ -5638,7 -4998,7 +5660,7 @@@ delta=0.02d0*pi escloc=0.0D0 do i=loc_start,loc_end - if (itype(i).eq.21) cycle + if (itype(i).eq.ntyp1) cycle costtab(i+1) =dcos(theta(i+1)) sinttab(i+1) =dsqrt(1-costtab(i+1)*costtab(i+1)) cost2tab(i+1)=dsqrt(0.5d0*(1.0d0+costtab(i+1))) @@@ -5647,7 -5007,7 +5669,7 @@@ cosfac=dsqrt(cosfac2) sinfac2=0.5d0/(1.0d0-costtab(i+1)) sinfac=dsqrt(sinfac2) - it=itype(i) + it=iabs(itype(i)) if (it.eq.10) goto 1 c C Compute the axes of tghe local cartesian coordinates system; store in @@@ -5665,7 -5025,7 +5687,7 @@@ C & dc_norm(3,i+nres y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac enddo do j = 1,3 - z_prime(j) = -uz(j,i-1) + z_prime(j) = -uz(j,i-1)*dsign(1.0d0,dfloat(itype(i))) enddo c write (2,*) "i",i c write (2,*) "x_prime",(x_prime(j),j=1,3) @@@ -5697,7 -5057,7 +5719,7 @@@ C Compute the energy of the ith side cbain C c write (2,*) "xx",xx," yy",yy," zz",zz - it=itype(i) + it=iabs(itype(i)) do j = 1,65 x(j) = sc_parmin(j,it) enddo @@@ -5705,7 -5065,7 +5727,7 @@@ Cc diagnostics - remove later xx1 = dcos(alph(2)) yy1 = dsin(alph(2))*dcos(omeg(2)) - zz1 = -dsin(alph(2))*dsin(omeg(2)) + zz1 = -dsign(1.0,dfloat(itype(i)))*dsin(alph(2))*dsin(omeg(2)) write(2,'(3f8.1,3f9.3,1x,3f9.3)') & alph(2)*rad2deg,omeg(2)*rad2deg,theta(3)*rad2deg,xx,yy,zz, & xx1,yy1,zz1 @@@ -5747,9 -5107,7 +5769,9 @@@ c & sumene4 c & dscp1,dscp2,sumene c sumene = enesc(x,xx,yy,zz,cost2tab(i+1),sint2tab(i+1)) escloc = escloc + sumene -c write (2,*) "i",i," escloc",sumene,escloc +c write (2,*) "i",i," escloc",sumene,escloc,it,itype(i) +c & ,zz,xx,yy +c#define DEBUG #ifdef DEBUG C C This section to check the numerical derivatives of the energy of ith side @@@ -5793,7 -5151,6 +5815,7 @@@ C End of diagnostics section C C Compute the gradient of esc C +c zz=zz*dsign(1.0,dfloat(itype(i))) pom_s1=(1.0d0+x(63))/(0.1d0 + dscp1)**2 pom_s16=6*(1.0d0+x(64))/(0.1d0 + dscp1**6)**2 pom_s2=(1.0d0+x(65))/(0.1d0 + dscp2)**2 @@@ -5818,7 -5175,7 +5840,7 @@@ & +(sumene2x+sumene4x*cost2tab(i+1))*(s2+s2_6) & +(pom1+pom2)*pom_dx #ifdef DEBUG - write(2,*), "de_dxx = ", de_dxx,de_dxx_num + write(2,*), "de_dxx = ", de_dxx,de_dxx_num,itype(i) #endif C sumene1y=x(3) + 2*x(6)*yy + x(9)*xx + x(10)*zz @@@ -5833,7 -5190,7 +5855,7 @@@ & +(sumene2y+sumene4y*cost2tab(i+1))*(s2+s2_6) & +(pom1-pom2)*pom_dy #ifdef DEBUG - write(2,*), "de_dyy = ", de_dyy,de_dyy_num + write(2,*), "de_dyy = ", de_dyy,de_dyy_num,itype(i) #endif C de_dzz =(x(24) +2*x(27)*zz +x(28)*xx +x(30)*yy @@@ -5845,16 -5202,15 +5867,16 @@@ & +x(60)*xx*yy)*cost2tab(i+1)*(s2+s2_6) & + ( x(14) + 2*x(17)*zz+ x(18)*xx + x(20)*yy)*(s2+s2_6) #ifdef DEBUG - write(2,*), "de_dzz = ", de_dzz,de_dzz_num + write(2,*), "de_dzz = ", de_dzz,de_dzz_num,itype(i) #endif C de_dt = 0.5d0*sumene3*cost2tab(i+1)*(s1+s1_6) & -0.5d0*sumene4*sint2tab(i+1)*(s2+s2_6) & +pom1*pom_dt1+pom2*pom_dt2 #ifdef DEBUG - write(2,*), "de_dt = ", de_dt,de_dt_num + write(2,*), "de_dt = ", de_dt,de_dt_num,itype(i) #endif +c#undef DEBUG c C cossc=scalar(dc_norm(1,i),dc_norm(1,i+nres)) @@@ -5879,16 -5235,13 +5901,16 @@@ c & (dC_norm(j,i-1),j=1,3)," vbld dZZ_Ci1(k)=0.0d0 dZZ_Ci(k)=0.0d0 do j=1,3 - dZZ_Ci(k)=dZZ_Ci(k)-uzgrad(j,k,2,i-1)*dC_norm(j,i+nres) - dZZ_Ci1(k)=dZZ_Ci1(k)-uzgrad(j,k,1,i-1)*dC_norm(j,i+nres) + dZZ_Ci(k)=dZZ_Ci(k)-uzgrad(j,k,2,i-1) + & *dsign(1.0d0,dfloat(itype(i)))*dC_norm(j,i+nres) + dZZ_Ci1(k)=dZZ_Ci1(k)-uzgrad(j,k,1,i-1) + & *dsign(1.0d0,dfloat(itype(i)))*dC_norm(j,i+nres) enddo dXX_XYZ(k)=vbld_inv(i+nres)*(x_prime(k)-xx*dC_norm(k,i+nres)) dYY_XYZ(k)=vbld_inv(i+nres)*(y_prime(k)-yy*dC_norm(k,i+nres)) - dZZ_XYZ(k)=vbld_inv(i+nres)*(z_prime(k)-zz*dC_norm(k,i+nres)) + dZZ_XYZ(k)=vbld_inv(i+nres)* + & (z_prime(k)-zz*dC_norm(k,i+nres)) c dt_dCi(k) = -dt_dCi(k)/sinttab(i+1) dt_dCi1(k)= -dt_dCi1(k)/sinttab(i+1) @@@ -6073,10 -5426,10 +6095,10 @@@ c lprn=.true etors=0.0D0 do i=iphi_start,iphi_end etors_ii=0.0D0 - if (itype(i-2).eq.21 .or. itype(i-1).eq.21 - & .or. itype(i).eq.21) cycle - itori=itortyp(itype(i-2)) - itori1=itortyp(itype(i-1)) + if (itype(i-2).eq.ntyp1.or. itype(i-1).eq.ntyp1 + & .or. itype(i).eq.ntyp1 .or. itype(i-3).eq.ntyp1) cycle + itori=itortyp(itype(i-2)) + itori1=itortyp(itype(i-1)) phii=phi(i) gloci=0.0D0 C Proline-Proline pair is a special case... @@@ -6170,29 -5523,17 +6192,29 @@@ C Set lprn=.true. for debuggin c lprn=.true. etors=0.0D0 do i=iphi_start,iphi_end - if (itype(i-2).eq.21 .or. itype(i-1).eq.21 - & .or. itype(i).eq.21) cycle - etors_ii=0.0D0 +C ANY TWO ARE DUMMY ATOMS in row CYCLE +c if (((itype(i-3).eq.ntyp1).and.(itype(i-2).eq.ntyp1)).or. +c & ((itype(i-2).eq.ntyp1).and.(itype(i-1).eq.ntyp1)) .or. +c & ((itype(i-1).eq.ntyp1).and.(itype(i).eq.ntyp1))) cycle + if (itype(i-2).eq.ntyp1.or. itype(i-1).eq.ntyp1 + & .or. itype(i).eq.ntyp1 .or. itype(i-3).eq.ntyp1) cycle +C In current verion the ALL DUMMY ATOM POTENTIALS ARE OFF +C For introducing the NH3+ and COO- group please check the etor_d for reference +C and guidance + etors_ii=0.0D0 + if (iabs(itype(i)).eq.20) then + iblock=2 + else + iblock=1 + endif itori=itortyp(itype(i-2)) itori1=itortyp(itype(i-1)) phii=phi(i) gloci=0.0D0 C Regular cosine and sine terms - do j=1,nterm(itori,itori1) - v1ij=v1(j,itori,itori1) - v2ij=v2(j,itori,itori1) + do j=1,nterm(itori,itori1,iblock) + v1ij=v1(j,itori,itori1,iblock) + v2ij=v2(j,itori,itori1,iblock) cosphi=dcos(j*phii) sinphi=dsin(j*phii) etors=etors+v1ij*cosphi+v2ij*sinphi @@@ -6207,7 -5548,7 +6229,7 @@@ C [v2 cos(phi/2)+v3 sin(phi/2) C cosphi=dcos(0.5d0*phii) sinphi=dsin(0.5d0*phii) - do j=1,nlor(itori,itori1) + do j=1,nlor(itori,itori1,iblock) vl1ij=vlor1(j,itori,itori1) vl2ij=vlor2(j,itori,itori1) vl3ij=vlor3(j,itori,itori1) @@@ -6220,14 -5561,13 +6242,14 @@@ gloci=gloci+vl1ij*(vl3ij*cosphi-vl2ij*sinphi)*pom enddo C Subtract the constant term - etors=etors-v0(itori,itori1) + etors=etors-v0(itori,itori1,iblock) if (energy_dec) write (iout,'(a6,i5,0pf7.3)') - & 'etor',i,etors_ii-v0(itori,itori1) + & 'etor',i,etors_ii-v0(itori,itori1,iblock) if (lprn) & write (iout,'(2(a3,2x,i3,2x),2i3,6f8.3/26x,6f8.3/)') & restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,itori,itori1, - & (v1(j,itori,itori1),j=1,6),(v2(j,itori,itori1),j=1,6) + & (v1(j,itori,itori1,iblock),j=1,6), + & (v2(j,itori,itori1,iblock),j=1,6) gloc(i-3,icg)=gloc(i-3,icg)+wtor*gloci c write (iout,*) 'i=',i,' gloc=',gloc(i-3,icg) enddo @@@ -6277,17 -5617,9 +6299,17 @@@ C Set lprn=.true. for debuggin lprn=.false. c lprn=.true. etors_d=0.0D0 +c write(iout,*) "a tu??" do i=iphid_start,iphid_end - if (itype(i-2).eq.21 .or. itype(i-1).eq.21 - & .or. itype(i).eq.21 .or. itype(i+1).eq.21) cycle +C ANY TWO ARE DUMMY ATOMS in row CYCLE +C if (((itype(i-3).eq.ntyp1).and.(itype(i-2).eq.ntyp1)).or. +C & ((itype(i-2).eq.ntyp1).and.(itype(i-1).eq.ntyp1)).or. +C & ((itype(i-1).eq.ntyp1).and.(itype(i).eq.ntyp1)) .or. +C & ((itype(i).eq.ntyp1).and.(itype(i+1).eq.ntyp1))) cycle + if ((itype(i-2).eq.ntyp1).or.itype(i-3).eq.ntyp1.or. + & (itype(i-1).eq.ntyp1).or.(itype(i).eq.ntyp1).or. + & (itype(i+1).eq.ntyp1)) cycle +C In current verion the ALL DUMMY ATOM POTENTIALS ARE OFF itori=itortyp(itype(i-2)) itori1=itortyp(itype(i-1)) itori2=itortyp(itype(i)) @@@ -6295,27 -5627,12 +6317,27 @@@ phii1=phi(i+1) gloci1=0.0D0 gloci2=0.0D0 + iblock=1 + if (iabs(itype(i+1)).eq.20) iblock=2 +C Iblock=2 Proline type +C ADASKO: WHEN PARAMETERS FOR THIS TYPE OF BLOCKING GROUP IS READY UNCOMMENT +C CHECK WEATHER THERE IS NECCESITY FOR iblock=3 for COO- +C if (itype(i+1).eq.ntyp1) iblock=3 +C The problem of NH3+ group can be resolved by adding new parameters please note if there +C IS or IS NOT need for this +C IF Yes uncomment below and add to parmread.F appropriate changes and to v1cij and so on +C is (itype(i-3).eq.ntyp1) ntblock=2 +C ntblock is N-terminal blocking group + C Regular cosine and sine terms - do j=1,ntermd_1(itori,itori1,itori2) - v1cij=v1c(1,j,itori,itori1,itori2) - v1sij=v1s(1,j,itori,itori1,itori2) - v2cij=v1c(2,j,itori,itori1,itori2) - v2sij=v1s(2,j,itori,itori1,itori2) + do j=1,ntermd_1(itori,itori1,itori2,iblock) +C Example of changes for NH3+ blocking group +C do j=1,ntermd_1(itori,itori1,itori2,iblock,ntblock) +C v1cij=v1c(1,j,itori,itori1,itori2,iblock,ntblock) + v1cij=v1c(1,j,itori,itori1,itori2,iblock) + v1sij=v1s(1,j,itori,itori1,itori2,iblock) + v2cij=v1c(2,j,itori,itori1,itori2,iblock) + v2sij=v1s(2,j,itori,itori1,itori2,iblock) cosphi1=dcos(j*phii) sinphi1=dsin(j*phii) cosphi2=dcos(j*phii1) @@@ -6325,12 -5642,12 +6347,12 @@@ gloci1=gloci1+j*(v1sij*cosphi1-v1cij*sinphi1) gloci2=gloci2+j*(v2sij*cosphi2-v2cij*sinphi2) enddo - do k=2,ntermd_2(itori,itori1,itori2) + do k=2,ntermd_2(itori,itori1,itori2,iblock) do l=1,k-1 - v1cdij = v2c(k,l,itori,itori1,itori2) - v2cdij = v2c(l,k,itori,itori1,itori2) - v1sdij = v2s(k,l,itori,itori1,itori2) - v2sdij = v2s(l,k,itori,itori1,itori2) + v1cdij = v2c(k,l,itori,itori1,itori2,iblock) + v2cdij = v2c(l,k,itori,itori1,itori2,iblock) + v1sdij = v2s(k,l,itori,itori1,itori2,iblock) + v2sdij = v2s(l,k,itori,itori1,itori2,iblock) cosphi1p2=dcos(l*phii+(k-l)*phii1) cosphi1m2=dcos(l*phii-(k-l)*phii1) sinphi1p2=dsin(l*phii+(k-l)*phii1) @@@ -6375,53 -5692,29 +6397,53 @@@ c amino-acid residues C Set lprn=.true. for debugging lprn=.false. c lprn=.true. -c write (iout,*) "EBACK_SC_COR",iphi_start,iphi_end,nterm_sccor +c write (iout,*) "EBACK_SC_COR",itau_start,itau_end esccor=0.0D0 - do i=iphi_start,iphi_end - if (itype(i-2).eq.21 .or. itype(i-1).eq.21) cycle + do i=itau_start,itau_end + if ((itype(i-2).eq.ntyp1).or.(itype(i-1).eq.ntyp1)) cycle esccor_ii=0.0D0 - itori=itype(i-2) - itori1=itype(i-1) + isccori=isccortyp(itype(i-2)) + isccori1=isccortyp(itype(i-1)) +c write (iout,*) "EBACK_SC_COR",i,nterm_sccor(isccori,isccori1) phii=phi(i) + do intertyp=1,3 !intertyp +cc Added 09 May 2012 (Adasko) +cc Intertyp means interaction type of backbone mainchain correlation: +c 1 = SC...Ca...Ca...Ca +c 2 = Ca...Ca...Ca...SC +c 3 = SC...Ca...Ca...SCi gloci=0.0D0 - do j=1,nterm_sccor - v1ij=v1sccor(j,itori,itori1) - v2ij=v2sccor(j,itori,itori1) - cosphi=dcos(j*phii) - sinphi=dsin(j*phii) + if (((intertyp.eq.3).and.((itype(i-2).eq.10).or. + & (itype(i-1).eq.10).or.(itype(i-2).eq.ntyp1).or. + & (itype(i-1).eq.ntyp1))) + & .or. ((intertyp.eq.1).and.((itype(i-2).eq.10) + & .or.(itype(i-2).eq.ntyp1).or.(itype(i-1).eq.ntyp1) + & .or.(itype(i).eq.ntyp1))) + & .or.((intertyp.eq.2).and.((itype(i-1).eq.10).or. + & (itype(i-1).eq.ntyp1).or.(itype(i-2).eq.ntyp1).or. + & (itype(i-3).eq.ntyp1)))) cycle + if ((intertyp.eq.2).and.(i.eq.4).and.(itype(1).eq.ntyp1)) cycle + if ((intertyp.eq.1).and.(i.eq.nres).and.(itype(nres).eq.ntyp1)) + & cycle + do j=1,nterm_sccor(isccori,isccori1) + v1ij=v1sccor(j,intertyp,isccori,isccori1) + v2ij=v2sccor(j,intertyp,isccori,isccori1) + cosphi=dcos(j*tauangle(intertyp,i)) + sinphi=dsin(j*tauangle(intertyp,i)) esccor=esccor+v1ij*cosphi+v2ij*sinphi gloci=gloci+j*(v2ij*cosphi-v1ij*sinphi) enddo +c write (iout,*) "EBACK_SC_COR",i,v1ij*cosphi+v2ij*sinphi,intertyp + gloc_sc(intertyp,i-3,icg)=gloc_sc(intertyp,i-3,icg)+wsccor*gloci if (lprn) & write (iout,'(2(a3,2x,i3,2x),2i3,6f8.3/26x,6f8.3/)') - & restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,itori,itori1, - & (v1sccor(j,itori,itori1),j=1,6),(v2sccor(j,itori,itori1),j=1,6) + & restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,isccori,isccori1, + & (v1sccor(j,intertyp,isccori,isccori1),j=1,6) + & ,(v2sccor(j,intertyp,isccori,isccori1),j=1,6) gsccor_loc(i-3)=gsccor_loc(i-3)+gloci + enddo !intertyp enddo + return end c---------------------------------------------------------------------------- @@@ -7426,7 -6719,7 +7448,7 @@@ C-------------------------------------- if (j.lt.nres-1) then itj1 = itortyp(itype(j+1)) else - itj1=ntortyp+1 + itj1=ntortyp endif do iii=1,2 dipi(iii,1)=Ub2(iii,i) @@@ -7516,14 -6809,14 +7538,14 @@@ C parallel orientation of the two CA-CA if (i.gt.1) then iti=itortyp(itype(i)) else - iti=ntortyp+1 + iti=ntortyp endif itk1=itortyp(itype(k+1)) itj=itortyp(itype(j)) if (l.lt.nres-1) then itl1=itortyp(itype(l+1)) else - itl1=ntortyp+1 + itl1=ntortyp endif C A1 kernel(j+1) A2T cd do iii=1,2 @@@ -7669,7 -6962,7 +7691,7 @@@ C Antiparallel orientation of the two C if (i.gt.1) then iti=itortyp(itype(i)) else - iti=ntortyp+1 + iti=ntortyp endif itk1=itortyp(itype(k+1)) itl=itortyp(itype(l)) @@@ -7677,7 -6970,7 +7699,7 @@@ if (j.lt.nres-1) then itj1=itortyp(itype(j+1)) else - itj1=ntortyp+1 + itj1=ntortyp endif C A2 kernel(j-1)T A1T call kernel(aa1(1,1),aa2t(1,1),a_chuj_der(1,1,1,1,jj,i), @@@ -8635,12 -7928,12 +8657,12 @@@ C o o C C \ /l\ /j\ / C C \ / \ / \ / C - C o| o | | o |o C + C o| o | | o |o C C \ j|/k\| \ |/k\|l C C \ / \ \ / \ C C o o C - C i i C - C C + C i i C + C C CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC cd write (2,*) 'eello6_graph2: i,',i,' j',j,' k',k,' l',l C AL 7/4/01 s1 would occur in the sixth-order moment, @@@ -8811,10 -8104,10 +8833,10 @@@ c-------------------------------------- double precision vv(2),pizda(2,2),auxmat(2,2),auxvec(2) logical swap CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC - C C + C C C Parallel Antiparallel C C C - C o o C + C o o C C /l\ / \ /j\ C C / \ / \ / \ C C /| o |o o| o |\ C @@@ -8831,14 -8124,14 +8853,14 @@@ C energy moment and not to th if (j.lt.nres-1) then itj1=itortyp(itype(j+1)) else - itj1=ntortyp+1 + itj1=ntortyp endif itk=itortyp(itype(k)) itk1=itortyp(itype(k+1)) if (l.lt.nres-1) then itl1=itortyp(itype(l+1)) else - itl1=ntortyp+1 + itl1=ntortyp endif #ifdef MOMENT s1=dip(4,jj,i)*dip(4,kk,k) @@@ -8928,7 -8221,7 +8950,7 @@@ c-------------------------------------- & auxvec1(2),auxmat1(2,2) logical swap CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC - C C + C C C Parallel Antiparallel C C C C o o C @@@ -8936,10 -8229,10 +8958,10 @@@ C /l\ / \ /j C / \ / \ / \ C C /| o |o o| o |\ C C \ j|/k\| \ |/k\|l C - C \ / \ \ / \ C + C \ / \ \ / \ C C o \ o \ C C i i C - C C + C C CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC C C 4/7/01 AL Component s1 was removed, because it pertains to the respective @@@ -8950,19 -8243,19 +8972,19 @@@ cd write (2,*) 'eello_graph4: wtur if (j.lt.nres-1) then itj1=itortyp(itype(j+1)) else - itj1=ntortyp+1 + itj1=ntortyp endif itk=itortyp(itype(k)) if (k.lt.nres-1) then itk1=itortyp(itype(k+1)) else - itk1=ntortyp+1 + itk1=ntortyp endif itl=itortyp(itype(l)) if (l.lt.nres-1) then itl1=itortyp(itype(l+1)) else - itl1=ntortyp+1 + itl1=ntortyp endif cd write (2,*) 'eello6_graph4:','i',i,' j',j,' k',k,' l',l cd write (2,*) 'iti',iti,' itj',itj,' itj1',itj1,' itk',itk, diff --combined source/unres/src_MD-M/geomout.F index 4673c4e,6fd71c5..266ad3d --- a/source/unres/src_MD-M/geomout.F +++ b/source/unres/src_MD-M/geomout.F @@@ -80,9 -80,15 +80,15 @@@ cmodel write (iunit,'(a5,i6)') 'MO if (nss.gt.0) then do i=1,nss + if (dyn_ss) then write(iunit,'(a6,i4,1x,a3,i7,4x,a3,i7)') - & 'SSBOND',i,'CYS',ihpb(i)-1-nres, - & 'CYS',jhpb(i)-1-nres + & 'SSBOND',i,'CYS',idssb(i)-nnt+1, + & 'CYS',jdssb(i)-nnt+1 + else + write(iunit,'(a6,i4,1x,a3,i7,4x,a3,i7)') + & 'SSBOND',i,'CYS',ihpb(i)-nnt+1-nres, + & 'CYS',jhpb(i)-nnt+1-nres + endif enddo endif @@@ -91,7 -97,7 +97,7 @@@ ires=0 do i=nnt,nct iti=itype(i) - if (iti.eq.21) then + if ((iti.eq.ntyp1).and.((itype(i+1)).eq.ntyp1)) then ichain=ichain+1 ires=0 write (iunit,'(a)') 'TER' @@@ -99,7 -105,6 +105,7 @@@ ires=ires+1 iatom=iatom+1 ica(i)=iatom + if (iti.ne.ntyp1) then write (iunit,10) iatom,restyp(iti),chainid(ichain), & ires,(c(j,i),j=1,3),vtot(i) if (iti.ne.10) then @@@ -107,18 -112,17 +113,18 @@@ write (iunit,20) iatom,restyp(iti),chainid(ichain), & ires,(c(j,nres+i),j=1,3), & vtot(i+nres) + endif endif endif enddo write (iunit,'(a)') 'TER' do i=nnt,nct-1 - if (itype(i).eq.21) cycle - if (itype(i).eq.10 .and. itype(i+1).ne.21) then + if (itype(i).eq.ntyp1) cycle + if (itype(i).eq.10 .and. itype(i+1).ne.ntyp1) then write (iunit,30) ica(i),ica(i+1) - else if (itype(i).ne.10 .and. itype(i+1).ne.21) then + else if (itype(i).ne.10 .and. itype(i+1).ne.ntyp1) then write (iunit,30) ica(i),ica(i+1),ica(i)+1 - else if (itype(i).ne.10 .and. itype(i+1).eq.21) then + else if (itype(i).ne.10 .and. itype(i+1).eq.ntyp1) then write (iunit,30) ica(i),ica(i)+1 endif enddo @@@ -126,7 -130,11 +132,11 @@@ write (iunit,30) ica(nct),ica(nct)+1 endif do i=1,nss + if (dyn_ss) then + write (iunit,30) ica(idssb(i))+1,ica(jdssb(i))+1 + else write (iunit,30) ica(ihpb(i)-nres)+1,ica(jhpb(i)-nres)+1 + endif enddo write (iunit,'(a6)') 'ENDMDL' 10 FORMAT ('ATOM',I7,' CA ',A3,1X,A1,I4,4X,3F8.3,f15.3) @@@ -202,7 -210,6 +212,7 @@@ c-------------------------------------- include 'COMMON.INTERACT' include 'COMMON.NAMES' include 'COMMON.GEO' + include 'COMMON.TORSION' write (iout,'(/a)') 'Geometry of the virtual chain.' write (iout,'(7a)') ' Res ',' d',' Theta', & ' Phi',' Dsc',' Alpha',' Omega' @@@ -281,8 -288,13 +291,13 @@@ c-------------------------------------- open(icart,file=cartname,access="append") #endif write (icart,'(e15.8,2e15.5,f12.5,$)') time,potE,uconst,t_bath - write (icart,'(i4,$)') + if (dyn_ss) then + write (icart,'(i4,$)') + & nss,(idssb(j)+nres,jdssb(j)+nres,j=1,nss) + else + write (icart,'(i4,$)') & nss,(ihpb(j),jhpb(j),j=1,nss) + endif write (icart,'(i4,20f7.4)') nfrag+npair+3*nfrag_back, & (qfrag(i),i=1,nfrag),(qpair(i),i=1,npair), & (utheta(i),ugamma(i),uscdiff(i),i=1,nfrag_back) @@@ -324,8 -336,13 +339,13 @@@ c-------------------------------------- call xdrffloat_(ixdrf, real(t_bath), iret) call xdrfint_(ixdrf, nss, iret) do j=1,nss + if (dyn_ss) then + call xdrfint_(ixdrf, idssb(j)+nres, iret) + call xdrfint_(ixdrf, jdssb(j)+nres, iret) + else call xdrfint_(ixdrf, ihpb(j), iret) call xdrfint_(ixdrf, jhpb(j), iret) + endif enddo call xdrfint_(ixdrf, nfrag+npair+3*nfrag_back, iret) do i=1,nfrag @@@ -348,8 -365,13 +368,13 @@@ call xdrffloat(ixdrf, real(t_bath), iret) call xdrfint(ixdrf, nss, iret) do j=1,nss + if (dyn_ss) then + call xdrfint(ixdrf, idssb(j)+nres, iret) + call xdrfint(ixdrf, jdssb(j)+nres, iret) + else call xdrfint(ixdrf, ihpb(j), iret) call xdrfint(ixdrf, jhpb(j), iret) + endif enddo call xdrfint(ixdrf, nfrag+npair+3*nfrag_back, iret) do i=1,nfrag diff --combined source/unres/src_MD-M/initialize_p.F index 1a5e34a,26ba786..818abde --- a/source/unres/src_MD-M/initialize_p.F +++ b/source/unres/src_MD-M/initialize_p.F @@@ -80,9 -80,7 +80,9 @@@ igeom= 8 intin= 9 ithep= 11 + ithep_pdb=51 irotam=12 + irotam_pdb=52 itorp= 13 itordp= 23 ielep= 14 @@@ -163,14 -161,10 +163,14 @@@ c call memmon_print_usage( rr0(i)=0.0D0 a0thet(i)=0.0D0 do j=1,2 - athet(j,i)=0.0D0 - bthet(j,i)=0.0D0 + do ichir1=-1,1 + do ichir2=-1,1 + athet(j,i,ichir1,ichir2)=0.0D0 + bthet(j,i,ichir1,ichir2)=0.0D0 + enddo + enddo enddo - do j=0,3 + do j=0,3 polthet(j,i)=0.0D0 enddo do j=1,3 @@@ -194,39 -188,15 +194,39 @@@ enddo nlob(ntyp1)=0 dsc(ntyp1)=0.0D0 - do i=1,maxtor - itortyp(i)=0 - do j=1,maxtor - do k=1,maxterm - v1(k,j,i)=0.0D0 - v2(k,j,i)=0.0D0 + do i=-maxtor,maxtor + itortyp(i)=0 +cc write (iout,*) "TU DOCHODZE",i,itortyp(i) + do iblock=1,2 + do j=-maxtor,maxtor + do k=1,maxterm + v1(k,j,i,iblock)=0.0D0 + v2(k,j,i,iblock)=0.0D0 enddo enddo + enddo enddo + do iblock=1,2 + do i=-maxtor,maxtor + do j=-maxtor,maxtor + do k=-maxtor,maxtor + do l=1,maxtermd_1 + v1c(1,l,i,j,k,iblock)=0.0D0 + v1s(1,l,i,j,k,iblock)=0.0D0 + v1c(2,l,i,j,k,iblock)=0.0D0 + v1s(2,l,i,j,k,iblock)=0.0D0 + enddo !l + do l=1,maxtermd_2 + do m=1,maxtermd_2 + v2c(m,l,i,j,k,iblock)=0.0D0 + v2s(m,l,i,j,k,iblock)=0.0D0 + enddo !m + enddo !l + enddo !k + enddo !j + enddo !i + enddo !iblock + do i=1,maxres itype(i)=0 itel(i)=0 @@@ -245,22 -215,6 +245,22 @@@ C Initialize the bridge array ihpb(i)=0 jhpb(i)=0 enddo +C Initialize correlation arrays + do i=-maxtor,maxtor + do k=1,2 + b1(k,i)=0.0 + b2(k,i)=0.0 + b1tilde(k,i)=0.0 +c b2tilde(k,i)=0.0 + do j=1,2 + CC(j,k,i)=0.0 + Ctilde(j,k,i)=0.0 + DD(j,k,i)=0.0 + Dtilde(j,k,i)=0.0 + EE(j,k,i)=0.0 + enddo + enddo + enddo C C Initialize timing. C @@@ -283,8 -237,8 +283,8 @@@ C Initialize constants used to split the energy into long- and short-range C components C - r_cut=2.0d0 - rlamb=0.3d0 +C r_cut=2.0d0 +C rlamb=0.3d0 #ifndef SPLITELE nprint_ene=nprint_ene-1 #endif @@@ -297,17 -251,11 +297,17 @@@ c-------------------------------------- include 'COMMON.NAMES' include 'COMMON.FFIELD' data restyp / + &'DD','DAU','DAI','DDB','DSM','DPR','DLY','DAR','DHI','DAS','DGL', + & 'DSG','DGN','DSN','DTH', + &'DYY','DAL','DTY','DTR','DVA','DLE','DIL','DPN','MED','DCY','ZER', &'CYS','MET','PHE','ILE','LEU','VAL','TRP','TYR','ALA','GLY','THR', - &'SER','GLN','ASN','GLU','ASP','HIS','ARG','LYS','PRO','D'/ + &'SER','GLN','ASN','GLU','ASP','HIS','ARG','LYS','PRO','SME','DBZ', + &'AIB','ABU','D'/ data onelet / + &'z','z','z','z','z','p','k','r','h','d','e','n','q','s','t','g', + &'a','y','w','v','l','i','f','m','c','x', &'C','M','F','I','L','V','W','Y','A','G','T', - &'S','Q','N','E','D','H','R','K','P','X'/ + &'S','Q','N','E','D','H','R','K','P','z','z','z','z','X'/ data potname /'LJ','LJK','BP','GB','GBV'/ data ename / & "EVDW SC-SC","EVDW2 SC-p","EES p-p","ECORR4 ","ECORR5 ", @@@ -393,6 -341,7 +393,7 @@@ cd write (iout,*) 'ns=',ns,' nss=',n cd & (ihpb(i),jhpb(i),i=1,nss) do i=nnt,nct-1 scheck=.false. + if (dyn_ss) goto 10 do ii=1,nss if (ihpb(ii).eq.i+nres) then scheck=.true. @@@ -612,9 -561,6 +613,9 @@@ C Partition local interaction iphi_end=iturn3_end+2 iturn3_start=iturn3_start-1 iturn3_end=iturn3_end-1 + call int_bounds(nres-3,itau_start,itau_end) + itau_start=itau_start+3 + itau_end=itau_end+3 call int_bounds(nres-3,iphi1_start,iphi1_end) iphi1_start=iphi1_start+3 iphi1_end=iphi1_end+3 @@@ -1143,8 -1089,6 +1144,8 @@@ c write (iout,*) "MPI_ROTAT2",MP idihconstr_end=ndih_constr iphid_start=iphi_start iphid_end=iphi_end-1 + itau_start=4 + itau_end=nres ibond_start=2 ibond_end=nres-1 ibondp_start=nnt diff --combined source/unres/src_MD-M/readrtns_CSA.F index 8e7b152,c2d0887..68d63c4 --- a/source/unres/src_MD-M/readrtns_CSA.F +++ b/source/unres/src_MD-M/readrtns_CSA.F @@@ -8,7 -8,6 +8,7 @@@ include 'COMMON.CONTROL' include 'COMMON.SBRIDGE' include 'COMMON.IOUNITS' + include 'COMMON.SPLITELE' logical file_exist C Read force-field parameters except weights call parmread @@@ -80,7 -79,6 +80,7 @@@ include 'COMMON.FFIELD' include 'COMMON.INTERACT' include 'COMMON.SETUP' + include 'COMMON.SPLITELE' COMMON /MACHSW/ KDIAG,ICORFL,IXDR character*8 diagmeth(0:3) /'Library','EVVRSP','Givens','Jacobi'/ character*80 ucase @@@ -215,15 -213,7 +215,15 @@@ cfmc modecalc=1 i2ndstr=index(controlcard,'USE_SEC_PRED') gradout=index(controlcard,'GRADOUT').gt.0 gnorm_check=index(controlcard,'GNORM_CHECK').gt.0 +C DISTCHAINMAX become obsolete for periodic boundry condition call reada(controlcard,'DISTCHAINMAX',distchainmax,5.0d0) +C Reading the dimensions of box in x,y,z coordinates + call reada(controlcard,'BOXX',boxxsize,100.0d0) + call reada(controlcard,'BOXY',boxysize,100.0d0) + call reada(controlcard,'BOXZ',boxzsize,100.0d0) +c Cutoff range for interactions + call reada(controlcard,"R_CUT",r_cut,15.0d0) + call reada(controlcard,"LAMBDA",rlamb,0.3d0) if (me.eq.king .or. .not.out1file ) & write (iout,*) "DISTCHAINMAX",distchainmax @@@ -305,11 -295,11 +305,11 @@@ cd endi do i=1,nrep iremd_m_total=iremd_m_total+remd_m(i) enddo - write (iout,*) 'Total number of replicas ',iremd_m_total + write (iout,*) 'Total number of replicas ',iremd_m_total + endif endif - endif if(me.eq.king.or..not.out1file) - & write (iout,'(/30(1h=),a,29(1h=)/)') " End of REMD run setup " + & write (iout,'(/30(1h=),a,29(1h=)/)') " End of REMD run setup " return end c-------------------------------------------------------------------------- @@@ -350,11 -340,12 +350,12 @@@ ntime_split0=ntime_split call readi(controlcard,"MAXTIME_SPLIT",maxtime_split,64) ntime_split0=ntime_split - call reada(controlcard,"R_CUT",r_cut,2.0d0) - call reada(controlcard,"LAMBDA",rlamb,0.3d0) +c call reada(controlcard,"R_CUT",r_cut,2.0d0) +c call reada(controlcard,"LAMBDA",rlamb,0.3d0) rest = index(controlcard,"REST").gt.0 tbf = index(controlcard,"TBF").gt.0 usampl = index(controlcard,"USAMPL").gt.0 + mdpdb = index(controlcard,"MDPDB").gt.0 call reada(controlcard,"T_BATH",t_bath,300.0d0) call reada(controlcard,"TAU_BATH",tau_bath,1.0d-1) @@@ -560,54 -551,54 +561,54 @@@ C Body C C Read weights of the subsequent energy terms. - call card_concat(weightcard) - call reada(weightcard,'WLONG',wlong,1.0D0) - call reada(weightcard,'WSC',wsc,wlong) - call reada(weightcard,'WSCP',wscp,wlong) - call reada(weightcard,'WELEC',welec,1.0D0) - call reada(weightcard,'WVDWPP',wvdwpp,welec) - call reada(weightcard,'WEL_LOC',wel_loc,1.0D0) - call reada(weightcard,'WCORR4',wcorr4,0.0D0) - call reada(weightcard,'WCORR5',wcorr5,0.0D0) - call reada(weightcard,'WCORR6',wcorr6,0.0D0) - call reada(weightcard,'WTURN3',wturn3,1.0D0) - call reada(weightcard,'WTURN4',wturn4,1.0D0) - call reada(weightcard,'WTURN6',wturn6,1.0D0) - call reada(weightcard,'WSCCOR',wsccor,1.0D0) - call reada(weightcard,'WSTRAIN',wstrain,1.0D0) - call reada(weightcard,'WBOND',wbond,1.0D0) - call reada(weightcard,'WTOR',wtor,1.0D0) - call reada(weightcard,'WTORD',wtor_d,1.0D0) - call reada(weightcard,'WANG',wang,1.0D0) - call reada(weightcard,'WSCLOC',wscloc,1.0D0) - call reada(weightcard,'SCAL14',scal14,0.4D0) - call reada(weightcard,'SCALSCP',scalscp,1.0d0) - call reada(weightcard,'CUTOFF',cutoff_corr,7.0d0) - call reada(weightcard,'DELT_CORR',delt_corr,0.5d0) - call reada(weightcard,'TEMP0',temp0,300.0d0) - if (index(weightcard,'SOFT').gt.0) ipot=6 + call card_concat(weightcard) + call reada(weightcard,'WLONG',wlong,1.0D0) + call reada(weightcard,'WSC',wsc,wlong) + call reada(weightcard,'WSCP',wscp,wlong) + call reada(weightcard,'WELEC',welec,1.0D0) + call reada(weightcard,'WVDWPP',wvdwpp,welec) + call reada(weightcard,'WEL_LOC',wel_loc,1.0D0) + call reada(weightcard,'WCORR4',wcorr4,0.0D0) + call reada(weightcard,'WCORR5',wcorr5,0.0D0) + call reada(weightcard,'WCORR6',wcorr6,0.0D0) + call reada(weightcard,'WTURN3',wturn3,1.0D0) + call reada(weightcard,'WTURN4',wturn4,1.0D0) + call reada(weightcard,'WTURN6',wturn6,1.0D0) + call reada(weightcard,'WSCCOR',wsccor,1.0D0) + call reada(weightcard,'WSTRAIN',wstrain,1.0D0) + call reada(weightcard,'WBOND',wbond,1.0D0) + call reada(weightcard,'WTOR',wtor,1.0D0) + call reada(weightcard,'WTORD',wtor_d,1.0D0) + call reada(weightcard,'WANG',wang,1.0D0) + call reada(weightcard,'WSCLOC',wscloc,1.0D0) + call reada(weightcard,'SCAL14',scal14,0.4D0) + call reada(weightcard,'SCALSCP',scalscp,1.0d0) + call reada(weightcard,'CUTOFF',cutoff_corr,7.0d0) + call reada(weightcard,'DELT_CORR',delt_corr,0.5d0) + call reada(weightcard,'TEMP0',temp0,300.0d0) + if (index(weightcard,'SOFT').gt.0) ipot=6 C 12/1/95 Added weight for the multi-body term WCORR - call reada(weightcard,'WCORRH',wcorr,1.0D0) - if (wcorr4.gt.0.0d0) wcorr=wcorr4 - weights(1)=wsc - weights(2)=wscp - weights(3)=welec - weights(4)=wcorr - weights(5)=wcorr5 - weights(6)=wcorr6 - weights(7)=wel_loc - weights(8)=wturn3 - weights(9)=wturn4 - weights(10)=wturn6 - weights(11)=wang - weights(12)=wscloc - weights(13)=wtor - weights(14)=wtor_d - weights(15)=wstrain - weights(16)=wvdwpp - weights(17)=wbond - weights(18)=scal14 - weights(21)=wsccor + call reada(weightcard,'WCORRH',wcorr,1.0D0) + if (wcorr4.gt.0.0d0) wcorr=wcorr4 + weights(1)=wsc + weights(2)=wscp + weights(3)=welec + weights(4)=wcorr + weights(5)=wcorr5 + weights(6)=wcorr6 + weights(7)=wel_loc + weights(8)=wturn3 + weights(9)=wturn4 + weights(10)=wturn6 + weights(11)=wang + weights(12)=wscloc + weights(13)=wtor + weights(14)=wtor_d + weights(15)=wstrain + weights(16)=wvdwpp + weights(17)=wbond + weights(18)=scal14 + weights(21)=wsccor if(me.eq.king.or..not.out1file) & write (iout,10) wsc,wscp,welec,wvdwpp,wbond,wang,wscloc,wtor, & wtor_d,wstrain,wel_loc,wcorr,wcorr5,wcorr6,wsccor,wturn3, @@@ -648,7 -639,7 +649,7 @@@ & 'General scaling factor of SC-p interactions:',scalscp endif r0_corr=cutoff_corr-delt_corr - do i=1,20 + do i=1,ntyp aad(i,1)=scalscp*aad(i,1) aad(i,2)=scalscp*aad(i,2) bad(i,1)=scalscp*bad(i,1) @@@ -689,13 -680,37 +690,37 @@@ call reada(weightcard,"V2SS",v2ss,7.61d0) call reada(weightcard,"V3SS",v3ss,13.7d0) call reada(weightcard,"EBR",ebr,-5.50D0) + dyn_ss=(index(weightcard,'DYN_SS').gt.0) + do i=1,maxres + dyn_ss_mask(i)=.false. + enddo + do i=1,maxres-1 + do j=i+1,maxres + dyn_ssbond_ij(i,j)=1.0d300 + enddo + enddo + call reada(weightcard,"HT",Ht,0.0D0) + if (dyn_ss) then + ss_depth=ebr/wsc-0.25*eps(1,1) + Ht=Ht/wsc-0.25*eps(1,1) + akcm=akcm*wstrain/wsc + akth=akth*wstrain/wsc + akct=akct*wstrain/wsc + v1ss=v1ss*wstrain/wsc + v2ss=v2ss*wstrain/wsc + v3ss=v3ss*wstrain/wsc + else + ss_depth=ebr/wstrain-0.25*eps(1,1)*wsc/wstrain + endif + if(me.eq.king.or..not.out1file) then write (iout,*) "Parameters of the SS-bond potential:" write (iout,*) "D0CM",d0cm," AKCM",akcm," AKTH",akth, & " AKCT",akct write (iout,*) "V1SS",v1ss," V2SS",v2ss," V3SS",v3ss - write (iout,*) "EBR",ebr - c print *,'indpdb=',indpdb,' pdbref=',pdbref + write (iout,*) "EBR",ebr," SS_DEPTH",ss_depth + write (iout,*)" HT",Ht + print *,'indpdb=',indpdb,' pdbref=',pdbref endif if (indpdb.gt.0 .or. pdbref) then read(inp,'(a)') pdbfile @@@ -727,7 -742,7 +752,7 @@@ c print *,'Finished reading pdb maxsi=1000 do i=2,nres-1 iti=itype(i) - if (iti.ne.10 .and. itype(i).ne.21) then + if (iti.ne.10 .and. itype(i).ne.ntyp1) then nsi=0 fail=.true. do while (fail.and.nsi.le.maxsi) @@@ -759,8 -774,8 +784,8 @@@ C Assign initial virtual bond length vbld_inv(i)=vblinv enddo do i=2,nres-1 - vbld(i+nres)=dsc(itype(i)) - vbld_inv(i+nres)=dsc_inv(itype(i)) + vbld(i+nres)=dsc(iabs(itype(i))) + vbld_inv(i+nres)=dsc_inv(iabs(itype(i))) c write (iout,*) "i",i," itype",itype(i), c & " dsc",dsc(itype(i))," vbld",vbld(i),vbld(i+nres) enddo @@@ -769,15 -784,15 +794,15 @@@ c print *,nre c print '(20i4)',(itype(i),i=1,nres) do i=1,nres #ifdef PROCOR - if (itype(i).eq.21 .or. itype(i+1).eq.21) then + if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) then #else - if (itype(i).eq.21) then + if (itype(i).eq.ntyp1) then #endif itel(i)=0 #ifdef PROCOR - else if (itype(i+1).ne.20) then + else if (iabs(itype(i+1)).ne.20) then #else - else if (itype(i).ne.20) then + else if (iabs(itype(i)).ne.20) then #endif itel(i)=1 else @@@ -834,8 -849,8 +859,8 @@@ C 8/13/98 Set limits to generating the #endif nct=nres cd print *,'NNT=',NNT,' NCT=',NCT - if (itype(1).eq.21) nnt=2 - if (itype(nres).eq.21) nct=nct-1 + if (itype(1).eq.ntyp1) nnt=2 + if (itype(nres).eq.ntyp1) nct=nct-1 if (pdbref) then if(me.eq.king.or..not.out1file) & write (iout,'(a,i3)') 'nsup=',nsup @@@ -952,7 -967,7 +977,7 @@@ C initial geometry enddo enddo do i=nnt,nct - if (itype(i).ne.10 .and. itype(i).ne.21) then + if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then do j=1,3 dc(j,i+nres)=c(j,i+nres)-c(j,i) dc_norm(j,i+nres)=dc_norm(j,i+nres)*vbld_inv(i+nres) @@@ -984,7 -999,6 +1009,7 @@@ enddo do i=2,nres-1 omeg(i)=-120d0*deg2rad + if (itype(i).le.0) omeg(i)=-omeg(i) enddo else if(me.eq.king.or..not.out1file) @@@ -1022,18 -1036,7 +1047,7 @@@ 40 continue endif #else - do itrial=1,100 - itmp=1 - call gen_rand_conf(itmp,*30) - goto 40 - 30 write (iout,*) 'Failed to generate random conformation', - & ', itrial=',itrial - write (*,*) 'Failed to generate random conformation', - & ', itrial=',itrial - enddo - write (iout,'(a,i3,a)') 'Processor:',me, - & ' error in generating random conformation.' - write (*,'(a,i3,a)') 'Processor:',me, + write (*,'(a)') & ' error in generating random conformation.' stop 40 continue @@@ -1065,18 -1068,35 +1079,35 @@@ C Generate distance constraints, if th write (iout,'(/a,i3,a)') & 'The chain contains',ns,' disulfide-bridging cysteines.' write (iout,'(20i4)') (iss(i),i=1,ns) + if (dyn_ss) then + write(iout,*)"Running with dynamic disulfide-bond formation" + else write (iout,'(/a/)') 'Pre-formed links are:' do i=1,nss i1=ihpb(i)-nres i2=jhpb(i)-nres it1=itype(i1) it2=itype(i2) - if (me.eq.king.or..not.out1file) - & write (iout,'(2a,i3,3a,i3,a,3f10.3)') + write (iout,'(2a,i3,3a,i3,a,3f10.3)') & restyp(it1),'(',i1,') -- ',restyp(it2),'(',i2,')',dhpb(i), & ebr,forcon(i) enddo write (iout,'(a)') + endif + endif + if (ns.gt.0.and.dyn_ss) then + do i=nss+1,nhpb + ihpb(i-nss)=ihpb(i) + jhpb(i-nss)=jhpb(i) + forcon(i-nss)=forcon(i) + dhpb(i-nss)=dhpb(i) + enddo + nhpb=nhpb-nss + nss=0 + call hpb_partition + do i=1,ns + dyn_ss_mask(iss(i))=.true. + enddo endif if (i2ndstr.gt.0) call secstrp2dihc c call geom_to_var(nvar,x) @@@ -1133,17 -1153,19 +1164,19 @@@ C Read information about disulfide brid include 'COMMON.SETUP' C Read bridging residues. read (inp,*) ns,(iss(i),i=1,ns) - c print *,'ns=',ns + print *,'ns=',ns if(me.eq.king.or..not.out1file) & write (iout,*) 'ns=',ns,' iss:',(iss(i),i=1,ns) C Check whether the specified bridging residues are cystines. do i=1,ns if (itype(iss(i)).ne.1) then if (me.eq.king.or..not.out1file) write (iout,'(2a,i3,a)') - & 'Do you REALLY think that the residue ',restyp(iss(i)),i, + & 'Do you REALLY think that the residue ', + & restyp(itype(iss(i))),i, & ' can form a disulfide bridge?!!!' write (*,'(2a,i3,a)') - & 'Do you REALLY think that the residue ',restyp(iss(i)),i, + & 'Do you REALLY think that the residue ', + & restyp(itype(iss(i))),i, & ' can form a disulfide bridge?!!!' #ifdef MPI call MPI_Finalize(MPI_COMM_WORLD,ierror) @@@ -1154,7 -1176,8 +1187,8 @@@ C Read preformed bridges. if (ns.gt.0) then read (inp,*) nss,(ihpb(i),jhpb(i),i=1,nss) - write (iout,*) 'nss=',nss,' ihpb,jhpb: ',(ihpb(i),jhpb(i),i=1,nss) + if(fg_rank.eq.0) + & write(iout,*)'nss=',nss,' ihpb,jhpb: ',(ihpb(i),jhpb(i),i=1,nss) if (nss.gt.0) then nhpb=nss C Check if the residues involved in bridges are in the specified list of @@@ -1222,7 -1245,7 +1256,7 @@@ enddo enddo do i=nnt,nct - if (itype(i).ne.10 .and. itype(i).ne.21) then + if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then do j=1,3 dc(j,i+nres)=c(j,i+nres)-c(j,i) dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres) @@@ -1302,7 -1325,7 +1336,7 @@@ C Set up variable list nvar=ntheta+nphi nside=0 do i=2,nres-1 - if (itype(i).ne.10 .and. itype(i).ne.21) then + if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then nside=nside+1 ialph(i,1)=nvar+nside ialph(nside,2)=i @@@ -1926,22 -1949,12 +1960,22 @@@ C Get parameter filenames and open the open (itordp,file=tordname,status='old',readonly) call getenv_loc('SCCORPAR',sccorname) open (isccor,file=sccorname,status='old',readonly) +#ifndef CRYST_THETA + call getenv_loc('THETPARPDB',thetname_pdb) + print *,"thetname_pdb ",thetname_pdb + open (ithep_pdb,file=thetname_pdb,status='old',action='read') + print *,ithep_pdb," opened" +#endif call getenv_loc('FOURIER',fouriername) open (ifourier,file=fouriername,status='old',readonly) call getenv_loc('ELEPAR',elename) open (ielep,file=elename,status='old',readonly) call getenv_loc('SIDEPAR',sidename) open (isidep,file=sidename,status='old',readonly) +#ifndef CRYST_SC + call getenv_loc('ROTPARPDB',rotname_pdb) + open (irotam_pdb,file=rotname_pdb,status='old',action='read') +#endif #endif #ifndef OLDSCP C @@@ -2012,7 -2025,7 +2046,7 @@@ c print *,"Processor",myrank," fg_ mol2name=prefix(:lenpre)//'_'//pot(:lenpot)//'.mol2' statname=prefix(:lenpre)//'_'//pot(:lenpot)//'.stat' if (lentmp.gt.0) - & call copy_to_tmp(pref_orig(:ile(pref_orig))//'_'//pot(:lenpot)// + & call copy_to_tmp(pref_orig(:ilen(pref_orig))//'_'//pot(:lenpot) & //'.stat') rest2name=prefix(:ilen(prefix))//'.rst' if(usampl) then @@@ -2103,8 -2116,6 +2137,8 @@@ C Write file name & thetname(:ilen(thetname)) write (iout,*) "Rotamer parameter file : ", & rotname(:ilen(rotname)) + write (iout,*) "Thetpdb parameter file : ", + & thetname_pdb(:ilen(thetname_pdb)) write (iout,*) "Threading database : ", & patname(:ilen(patname)) if (lentmp.ne.0) @@@ -2246,11 -2257,11 +2280,11 @@@ c write (iout,*) i,ifrag_(1,i),i c write (iout,*) "j",j," k",k ddjk=dist(j,k) if (constr_dist.eq.1) then - nhpb=nhpb+1 - ihpb(nhpb)=j - jhpb(nhpb)=k + nhpb=nhpb+1 + ihpb(nhpb)=j + jhpb(nhpb)=k dhpb(nhpb)=ddjk - forcon(nhpb)=wfrag_(i) + forcon(nhpb)=wfrag_(i) else if (constr_dist.eq.2) then if (ddjk.le.dist_cut) then nhpb=nhpb+1 @@@ -2428,7 -2439,7 +2462,7 @@@ #endif if (OKRandom) then c r1 = prng_next(me) - r1=ran_number(0.0D0,1.0D0) + r1=ran_number(0.0D0,1.0D0) if(me.eq.king) & write (iout,*) 'ran_num',r1 if (r1.lt.0.0d0) OKRandom=.false. diff --combined source/unres/src_MD-M/sc_move.F index 2082e98,b6837fd..274767b --- a/source/unres/src_MD-M/sc_move.F +++ b/source/unres/src_MD-M/sc_move.F @@@ -15,7 -15,9 +15,9 @@@ crc implicit non c Includes implicit real*8 (a-h,o-z) include 'DIMENSIONS' + #ifdef MPI include 'mpif.h' + #endif include 'COMMON.GEO' include 'COMMON.VAR' include 'COMMON.HEADER' @@@ -211,7 -213,7 +213,7 @@@ c Define what is meant by "neighbou c Don't do glycine or ends i=itype(res_pick) - if (i.eq.10 .or. i.eq.21) return + if (i.eq.10 .or. i.eq.ntyp1) return c Freeze everything (later will relax only selected side-chains) mask_r=.true. @@@ -253,7 -255,7 +255,7 @@@ cd print *,'new ',(energy(k) n_try=0 do while (n_try.lt.n_maxtry .and. orig_e-cur_e.lt.e_drop) c Move the selected residue (don't worry if it fails) - call gen_side(itype(res_pick),theta(res_pick+1), + call gen_side(iabs(itype(res_pick)),theta(res_pick+1), + alph(res_pick),omeg(res_pick),fail) c Minimize the side-chains starting from the new arrangement @@@ -717,8 -719,8 +719,8 @@@ c if (icall.eq.0) lprn=.true do i=iatsc_s,iatsc_e - itypi=itype(i) - itypi1=itype(i+1) + itypi=iabs(itype(i)) + itypi1=iabs(itype(i+1)) xi=c(1,nres+i) yi=c(2,nres+i) zi=c(3,nres+i) @@@ -733,7 -735,7 +735,7 @@@ do j=istart(i,iint),iend(i,iint) IF (mask_side(j).eq.1.or.mask_side(i).eq.1) THEN ind=ind+1 - itypj=itype(j) + itypj=iabs(itype(j)) dscj_inv=dsc_inv(itypj) sig0ij=sigma(itypi,itypj) chi1=chi(itypi,itypj) diff --combined source/unres/src_MD-M/unres.F index 83afd9f,b1ddb28..4903ec0 --- a/source/unres/src_MD-M/unres.F +++ b/source/unres/src_MD-M/unres.F @@@ -103,7 -103,12 +103,12 @@@ C Fine-grain slaves just do energy and else if (modecalc.eq.12) then call exec_MD else if (modecalc.eq.14) then + #ifdef MPI call exec_MREMD + #else + write (iout,*) "Need a parallel version to run MREMD." + stop + #endif else write (iout,'(a)') 'This calculation type is not supported', & ModeCalc @@@ -139,6 -144,7 +144,7 @@@ c-------------------------------------- return end c--------------------------------------------------------------------------- + #ifdef MPI subroutine exec_MREMD include 'DIMENSIONS' #ifdef MPI @@@ -163,6 -169,7 +169,7 @@@ endif return end + #endif c--------------------------------------------------------------------------- subroutine exec_eeval_or_minim implicit real*8 (a-h,o-z) @@@ -189,16 -196,13 +196,25 @@@ double precision energy(0:n_ene) double precision energy_long(0:n_ene),energy_short(0:n_ene) double precision varia(maxvar) ++<<<<<<< HEAD + if (indpdb.eq.0) call chainbuild + time00=MPI_Wtime() + print *,'dc',c(1,1) + if (indpdb.ne.0) then + dc(1,0)=c(1,1) + dc(2,0)=c(2,1) + dc(3,0)=c(3,1) + endif ++======= + if (indpdb.eq.0) call chainbuild + #ifdef MPI + time00=MPI_Wtime() + #else + time00=tcpu() + #endif ++>>>>>>> f5379d3246c4bd95e946c4d35d4a1c13e329c4cb call chainbuild_cart + print *,'dc',dc(1,0),dc(2,0),dc(3,0) if (split_ene) then print *,"Processor",myrank," after chainbuild" icall=1 @@@ -216,16 -220,18 +232,20 @@@ call enerprint(energy(0)) endif call etotal(energy(0)) + #ifdef MPI time_ene=MPI_Wtime()-time00 + #else + time_ene=tcpu()-time00 + #endif write (iout,*) "Time for energy evaluation",time_ene print *,"after etotal" etota = energy(0) etot =etota call enerprint(energy(0)) call hairpin(.true.,nharp,iharp) + print *,'after hairpin' call secondary2(.true.) + print *,'after secondary' if (minim) then crc overlap test if (overlapsc) then @@@ -241,7 -247,11 +261,11 @@@ if (dccart) then print *, 'Calling MINIM_DC' + #ifdef MPI time1=MPI_WTIME() + #else + time1=tcpu() + #endif call minim_dc(etot,iretcode,nfun) else if (indpdb.ne.0) then @@@ -250,17 -260,23 +274,25 @@@ endif call geom_to_var(nvar,varia) print *,'Calling MINIMIZE.' + #ifdef MPI time1=MPI_WTIME() + #else + time1=tcpu() + #endif call minimize(etot,varia,iretcode,nfun) endif print *,'SUMSL return code is',iretcode,' eval ',nfun + #ifdef MPI evals=nfun/(MPI_WTIME()-time1) + #else + evals=nfun/(tcpu()-time1) + #endif print *,'# eval/s',evals print *,'refstr=',refstr - call hairpin(.true.,nharp,iharp) + call hairpin(.false.,nharp,iharp) + print *,'after hairpin' call secondary2(.true.) + print *,'after secondary' call etotal(energy(0)) etot = energy(0) call enerprint(energy(0)) @@@ -622,7 -638,7 +654,7 @@@ c Broadcast the order to compute intern endif do while (.not. eof) if (read_cart) then - read (intin,'(e15.10,e15.5)',end=1100,err=1100) time,ene + read (intin,'(e15.10,e15.5)',end=11,err=11) time,ene call read_x(intin,*11) #ifdef MPI c Broadcast the order to compute internal coordinates to the slaves. @@@ -631,7 -647,7 +663,7 @@@ #endif call int_from_cart1(.false.) else - read (intin,'(i5)',end=1100,err=1100) iconf + read (intin,'(i5)',end=11,err=11) iconf call read_angles(intin,*11) call geom_to_var(nvar,varia) call chainbuild diff --combined source/unres/src_MD/CMakeLists.txt index dea499c,ea7776c..8d21134 --- a/source/unres/src_MD/CMakeLists.txt +++ b/source/unres/src_MD/CMakeLists.txt @@@ -59,6 -59,7 +59,7 @@@ set(UNRES_MD_SRC parmread.F pinorm.f printmat.f + prng_32.F q_measure.F randgens.f rattle.F @@@ -81,19 -82,6 +82,6 @@@ ssMD.F ) - if(Fortran_COMPILER_NAME STREQUAL "ifort") - set(UNRES_MD_SRC0 ${UNRES_MD_SRC0} prng.f ) - elseif(Fortran_COMPILER_NAME STREQUAL "mpif90") - set(UNRES_MD_SRC0 ${UNRES_MD_SRC0} prng.f ) - elseif(Fortran_COMPILER_NAME STREQUAL "f95") - set(UNRES_MD_SRC0 ${UNRES_MD_SRC0} prng.f ) - elseif(Fortran_COMPILER_NAME STREQUAL "gfortran") - set(UNRES_MD_SRC0 ${UNRES_MD_SRC0} prng.f ) - else() - set(UNRES_MD_SRC0 ${UNRES_MD_SRC0} prng_32.F ) - endif (Fortran_COMPILER_NAME STREQUAL "ifort") - - set(UNRES_MD_SRC3 energy_p_new_barrier.F energy_p_new-sep_barrier.F @@@ -124,6 -112,7 +112,7 @@@ set(UNRES_MD_PP_SR MP.F MREMD.F parmread.F + prng_32.F q_measure1.F q_measure3.F q_measure.F @@@ -141,11 -130,6 +130,6 @@@ proc_proc.c ) - - if(NOT Fortran_COMPILER_NAME STREQUAL "ifort") - set(UNRES_MD_PP_SRC ${UNRES_MD_PP_SRC} prng_32.F) - endif(NOT Fortran_COMPILER_NAME STREQUAL "ifort") - #================================================ # Set comipiler flags for different sourcefiles #================================================ @@@ -161,20 -145,15 +145,20 @@@ elseif (Fortran_COMPILER_NAME STREQUAL set(FFLAGS2 "-std=legacy -I. ") #set(FFLAGS3 "-c -w -O3 -ipo -ipo_obj -opt_report" ) set(FFLAGS3 "-std=legacy -I. " ) +elseif (Fortran_COMPILER_NAME STREQUAL "g77") + set(FFLAGS0 "-I ${CMAKE_CURRENT_SOURCE_DIR} " ) + set(FFLAGS1 "-g -I ${CMAKE_CURRENT_SOURCE_DIR} " ) + set(FFLAGS2 "-I ${CMAKE_CURRENT_SOURCE_DIR} ") + set(FFLAGS3 "-I ${CMAKE_CURRENT_SOURCE_DIR} " ) endif (Fortran_COMPILER_NAME STREQUAL "ifort") # Add MPI compiler flags if(UNRES_WITH_MPI) - set(FFLAGS0 "${FFLAGS0} -I${MPIF_INCLUDE_DIRECTORIES}") - set(FFLAGS1 "${FFLAGS1} -I${MPIF_INCLUDE_DIRECTORIES}") - set(FFLAGS2 "${FFLAGS2} -I${MPIF_INCLUDE_DIRECTORIES}") - set(FFLAGS3 "${FFLAGS3} -I${MPIF_INCLUDE_DIRECTORIES}") + set(FFLAGS0 "${FFLAGS0} -I${MPI_Fortran_INCLUDE_PATH}") + set(FFLAGS1 "${FFLAGS1} -I${MPI_Fortran_INCLUDE_PATH}") + set(FFLAGS2 "${FFLAGS2} -I${MPI_Fortran_INCLUDE_PATH}") + set(FFLAGS3 "${FFLAGS3} -I${MPI_Fortran_INCLUDE_PATH}") endif(UNRES_WITH_MPI) set_property(SOURCE ${UNRES_MD_SRC0} APPEND PROPERTY COMPILE_FLAGS ${FFLAGS0} ) @@@ -187,14 -166,14 +171,14 @@@ set_property(SOURCE ${UNRES_MD_SRC3} PR #========================================= if(UNRES_MD_FF STREQUAL "GAB" ) # set preprocesor flags - set(CPPFLAGS "PROCOR -DUNRES -DISNAN -DSPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC" ) + set(CPPFLAGS "PROCOR -DUNRES -DISNAN -DSPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -DSCCORPDB" ) #========================================= # Settings for E0LL2Y force field #========================================= elseif(UNRES_MD_FF STREQUAL "E0LL2Y") # set preprocesor flags - set(CPPFLAGS "PROCOR -DUNRES -DISNAN -DSPLITELE -DLANG0" ) + set(CPPFLAGS "PROCOR -DUNRES -DISNAN -DSPLITELE -DLANG0 -DSCCORPDB" ) endif(UNRES_MD_FF STREQUAL "GAB") #========================================= @@@ -217,12 -196,6 +201,12 @@@ elseif (Fortran_COMPILER_NAME STREQUAL elseif (Fortran_COMPILER_NAME STREQUAL "gfortran") # Add old gfortran flags set(CPPFLAGS "${CPPFLAGS} -DG77") +elseif (Fortran_COMPILER_NAME STREQUAL "g77") + # Add old gfortran flags + set(CPPFLAGS "${CPPFLAGS} -DG77") +else(Fortran_COMPILER_NAME STREQUAL "ifort") + # Default preprocessor flag + set(CPPFLAGS "${CPPFLAGS} -DPGI") endif (Fortran_COMPILER_NAME STREQUAL "ifort") #========================================= @@@ -233,6 -206,13 +217,13 @@@ if (UNRES_WITH_MPI endif(UNRES_WITH_MPI) #========================================= + # Add 64-bit specific preprocessor flags + #========================================= + if (architektura STREQUAL "64") + set(CPPFLAGS "${CPPFLAGS} -DAMD64") + endif (architektura STREQUAL "64") + + #========================================= # Apply preprocesor flags to *.F files #========================================= set_property(SOURCE ${UNRES_MD_PP_SRC} PROPERTY COMPILE_DEFINITIONS ${CPPFLAGS} ) @@@ -243,10 -223,10 +234,10 @@@ #======================================== if(UNRES_WITH_MPI) # binary with mpi - set(UNRES_BIN "unres_${Fortran_COMPILER_NAME}_MPICH_${UNRES_MD_FF}.exe") + set(UNRES_BIN "unresMD_${Fortran_COMPILER_NAME}_MPICH_${UNRES_MD_FF}.exe") else(UNRES_WITH_MPI) # binary without mpi - set(UNRES_BIN "unres_${Fortran_COMPILER_NAME}_single_${UNRES_MD_FF}.exe") + set(UNRES_BIN "unresMD_${Fortran_COMPILER_NAME}_single_${UNRES_MD_FF}.exe") endif(UNRES_WITH_MPI) #========================================= @@@ -292,7 -272,7 +283,7 @@@ set(UNRES_MD_SRCS ${UNRES_MD_SRC0} ${UN #========================================= add_executable(UNRES_BIN-MD ${UNRES_MD_SRCS} ) set_target_properties(UNRES_BIN-MD PROPERTIES OUTPUT_NAME ${UNRES_BIN}) - #set_property(TARGET ${UNRES_BIN} PROPERTY RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin/unres/MD ) + set_property(TARGET UNRES_BIN-MD PROPERTY RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin ) #add_dependencies (${UNRES_BIN} ${UNRES_XDRFLIB}) @@@ -301,13 -281,18 +292,18 @@@ #========================================= # link MPI library (libmpich.a) if(UNRES_WITH_MPI) - target_link_libraries( UNRES_BIN-MD ${MPIF_LIBRARIES} ) + target_link_libraries( UNRES_BIN-MD ${MPI_Fortran_LIBRARIES} ) endif(UNRES_WITH_MPI) # link libxdrf.a #message("UNRES_XDRFLIB=${UNRES_XDRFLIB}") target_link_libraries( UNRES_BIN-MD xdrf ) #========================================= + # Install Path + #========================================= + install(TARGETS UNRES_BIN-MD DESTINATION ${CMAKE_INSTALL_PREFIX}) + + #========================================= # TESTS #========================================= @@@ -337,7 -322,7 +333,7 @@@ FILE(WRITE ${CMAKE_CURRENT_BINARY_DIR}/ export POT=GB export PREFIX=ala10 #----------------------------------------------------------------------------- - UNRES_BIN=./${UNRES_BIN} + UNRES_BIN=${CMAKE_BINARY_DIR}/bin/${UNRES_BIN} #----------------------------------------------------------------------------- DD=${CMAKE_SOURCE_DIR}/PARAM export BONDPAR=$DD/bond.parm diff --combined source/unres/src_MD/COMMON.SCCOR index 154de36,8de6d3c..7952bd1 --- a/source/unres/src_MD/COMMON.SCCOR +++ b/source/unres/src_MD/COMMON.SCCOR @@@ -2,17 -2,16 +2,17 @@@ cc Parameters of the SCCOR ter double precision v1sccor,v2sccor,vlor1sccor, & vlor2sccor,vlor3sccor,gloc_sc, & dcostau,dsintau,dtauangle,dcosomicron, - & domicron + & domicron,v0sccor integer nterm_sccor,isccortyp,nsccortyp,nlor_sccor - common/sccor/v1sccor(maxterm_sccor,3,20,20), - & v2sccor(maxterm_sccor,3,20,20), + common/sccor/v1sccor(maxterm_sccor,3,-ntyp:ntyp,-ntyp:ntyp), + & v2sccor(maxterm_sccor,3,-ntyp:ntyp,-ntyp:ntyp), + & v0sccor(maxterm_sccor,-ntyp:ntyp,-ntyp:ntyp), + & nterm_sccor(-ntyp:ntyp,-ntyp:ntyp),isccortyp(-ntyp:ntyp), + & nsccortyp, + & nlor_sccor(-ntyp:ntyp,-ntyp:ntyp), & vlor1sccor(maxterm_sccor,20,20), & vlor2sccor(maxterm_sccor,20,20), & vlor3sccor(maxterm_sccor,20,20),gloc_sc(3,0:maxres2,10), - & v0sccor(ntyp,ntyp), & dcostau(3,3,3,maxres2),dsintau(3,3,3,maxres2), & dtauangle(3,3,3,maxres2),dcosomicron(3,3,3,maxres2), - & domicron(3,3,3,maxres2), - & nterm_sccor(ntyp,ntyp),isccortyp(ntyp),nsccortyp, - & nlor_sccor(ntyp,ntyp) + & domicron(3,3,3,maxres2) diff --combined source/unres/src_MD/energy_p_new_barrier.F index 7cf6721,4f753e4..33b9ff7 --- a/source/unres/src_MD/energy_p_new_barrier.F +++ b/source/unres/src_MD/energy_p_new_barrier.F @@@ -1449,7 -1449,7 +1449,7 @@@ do iint=1,nint_gr(i) do j=istart(i,iint),iend(i,iint) ind=ind+1 - itypj=itype(j) + itypj=iabs(itype(j)) c dscj_inv=dsc_inv(itypj) dscj_inv=vbld_inv(j+nres) chi1=chi(itypi,itypj) @@@ -1592,22 -1592,7 +1592,22 @@@ evdw=evdw+evdwij if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a3)') & 'evdw',i,j,evdwij,' ss' +C triple bond artifac removal + do k=j+1,iend(i,iint) +C search over all next residues + if (dyn_ss_mask(k)) then +C check if they are cysteins +C write(iout,*) 'k=',k + call triple_ssbond_ene(i,j,k,evdwij) +C call the energy function that removes the artifical triple disulfide +C bond the soubroutine is located in ssMD.F + evdw=evdw+evdwij + if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a3)') + & 'evdw',i,j,evdwij,'tss' + endif!dyn_ss_mask(k) + enddo! k ELSE +C cycle ind=ind+1 itypj=itype(j) c dscj_inv=dsc_inv(itypj) @@@ -4584,18 -4569,6 +4584,18 @@@ c write (*,'(a,i2)') 'EBEND ICG=',i C Zero the energy function and its derivative at 0 or pi. call splinthet(theta(i),0.5d0*delta,ss,ssd) it=itype(i-1) + ichir1=isign(1,itype(i-2)) + ichir2=isign(1,itype(i)) + if (itype(i-2).eq.10) ichir1=isign(1,itype(i-1)) + if (itype(i).eq.10) ichir2=isign(1,itype(i-1)) + if (itype(i-1).eq.10) then + itype1=isign(10,itype(i-2)) + ichir11=isign(1,itype(i-2)) + ichir12=isign(1,itype(i-2)) + itype2=isign(10,itype(i)) + ichir21=isign(1,itype(i)) + ichir22=isign(1,itype(i)) + endif if (i.gt.3) then #ifdef OSF phii=phi(i) @@@ -4629,27 -4602,15 +4629,27 @@@ C dependent on the adjacent virtual-bon C In following comments this theta will be referred to as t_c. thet_pred_mean=0.0d0 do k=1,2 - athetk=athet(k,it) - bthetk=bthet(k,it) + athetk=athet(k,it,ichir1,ichir2) + bthetk=bthet(k,it,ichir1,ichir2) + if (it.eq.10) then + athetk=athet(k,itype1,ichir11,ichir12) + bthetk=bthet(k,itype2,ichir21,ichir22) + endif thet_pred_mean=thet_pred_mean+athetk*y(k)+bthetk*z(k) enddo dthett=thet_pred_mean*ssd thet_pred_mean=thet_pred_mean*ss+a0thet(it) C Derivatives of the "mean" values in gamma1 and gamma2. - dthetg1=(-athet(1,it)*y(2)+athet(2,it)*y(1))*ss - dthetg2=(-bthet(1,it)*z(2)+bthet(2,it)*z(1))*ss + dthetg1=(-athet(1,it,ichir1,ichir2)*y(2) + &+athet(2,it,ichir1,ichir2)*y(1))*ss + dthetg2=(-bthet(1,it,ichir1,ichir2)*z(2) + & +bthet(2,it,ichir1,ichir2)*z(1))*ss + if (it.eq.10) then + dthetg1=(-athet(1,itype1,ichir11,ichir12)*y(2) + &+athet(2,itype1,ichir11,ichir12)*y(1))*ss + dthetg2=(-bthet(1,itype2,ichir21,ichir22)*z(2) + & +bthet(2,itype2,ichir21,ichir22)*z(1))*ss + endif if (theta(i).gt.pi-delta) then call theteng(pi-delta,thet_pred_mean,theta0(it),f0,fprim0, & E_tc0) @@@ -4847,9 -4808,6 +4847,9 @@@ enddo endif if (i.lt.nres) then + + if (iabs(itype(i+1)).eq.20) iblock=2 + if (iabs(itype(i+1)).ne.20) iblock=1 #ifdef OSF phii1=phi(i+1) if (phii1.ne.phii1) phii1=150.0 @@@ -4870,7 -4828,7 +4870,7 @@@ sinph2(k)=0.0d0 enddo endif - ethetai=aa0thet(ityp1,ityp2,ityp3) + ethetai=aa0thet(ityp1,ityp2,ityp3,iblock) do k=1,ndouble do l=1,k-1 ccl=cosph1(l)*cosph2(k-l) @@@ -4892,12 -4850,11 +4892,12 @@@ enddo endif do k=1,ntheterm - ethetai=ethetai+aathet(k,ityp1,ityp2,ityp3)*sinkt(k) - dethetai=dethetai+0.5d0*k*aathet(k,ityp1,ityp2,ityp3) + ethetai=ethetai+aathet(k,ityp1,ityp2,ityp3,iblock)*sinkt(k) + dethetai=dethetai+0.5d0*k*aathet(k,ityp1,ityp2,ityp3,iblock) & *coskt(k) if (lprn) - & write (iout,*) "k",k," aathet",aathet(k,ityp1,ityp2,ityp3), + & write (iout,*) "k",k, + & "aathet",aathet(k,ityp1,ityp2,ityp3,iblock), & " ethetai",ethetai enddo if (lprn) then @@@ -4916,24 -4873,24 +4916,24 @@@ endif do m=1,ntheterm2 do k=1,nsingle - aux=bbthet(k,m,ityp1,ityp2,ityp3)*cosph1(k) - & +ccthet(k,m,ityp1,ityp2,ityp3)*sinph1(k) - & +ddthet(k,m,ityp1,ityp2,ityp3)*cosph2(k) - & +eethet(k,m,ityp1,ityp2,ityp3)*sinph2(k) + aux=bbthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph1(k) + & +ccthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph1(k) + & +ddthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph2(k) + & +eethet(k,m,ityp1,ityp2,ityp3,iblock)*sinph2(k) ethetai=ethetai+sinkt(m)*aux dethetai=dethetai+0.5d0*m*aux*coskt(m) dephii=dephii+k*sinkt(m)*( - & ccthet(k,m,ityp1,ityp2,ityp3)*cosph1(k)- - & bbthet(k,m,ityp1,ityp2,ityp3)*sinph1(k)) + & ccthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph1(k)- + & bbthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph1(k)) dephii1=dephii1+k*sinkt(m)*( - & eethet(k,m,ityp1,ityp2,ityp3)*cosph2(k)- - & ddthet(k,m,ityp1,ityp2,ityp3)*sinph2(k)) + & eethet(k,m,ityp1,ityp2,ityp3,iblock)*cosph2(k)- + & ddthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph2(k)) if (lprn) & write (iout,*) "m",m," k",k," bbthet", - & bbthet(k,m,ityp1,ityp2,ityp3)," ccthet", - & ccthet(k,m,ityp1,ityp2,ityp3)," ddthet", - & ddthet(k,m,ityp1,ityp2,ityp3)," eethet", - & eethet(k,m,ityp1,ityp2,ityp3)," ethetai",ethetai + & bbthet(k,m,ityp1,ityp2,ityp3,iblock)," ccthet", + & ccthet(k,m,ityp1,ityp2,ityp3,iblock)," ddthet", + & ddthet(k,m,ityp1,ityp2,ityp3,iblock)," eethet", + & eethet(k,m,ityp1,ityp2,ityp3,iblock)," ethetai",ethetai enddo enddo if (lprn) @@@ -4941,33 -4898,28 +4941,33 @@@ do m=1,ntheterm3 do k=2,ndouble do l=1,k-1 - aux=ffthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)+ - & ffthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l)+ - & ggthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)+ - & ggthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l) + aux=ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)+ + & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l)+ + & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)+ + & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l) + ethetai=ethetai+sinkt(m)*aux dethetai=dethetai+0.5d0*m*coskt(m)*aux dephii=dephii+l*sinkt(m)*( - & -ffthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)- - & ffthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)+ - & ggthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)+ - & ggthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l)) + & -ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)- + & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l)+ + & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)+ + & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l)) + dephii1=dephii1+(k-l)*sinkt(m)*( - & -ffthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)+ - & ffthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)+ - & ggthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)- - & ggthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l)) + &-ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)+ + & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l)+ + & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)- + & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l)) + if (lprn) then write (iout,*) "m",m," k",k," l",l," ffthet", - & ffthet(l,k,m,ityp1,ityp2,ityp3), - & ffthet(k,l,m,ityp1,ityp2,ityp3)," ggthet", - & ggthet(l,k,m,ityp1,ityp2,ityp3), - & ggthet(k,l,m,ityp1,ityp2,ityp3)," ethetai",ethetai + & ffthet(l,k,m,ityp1,ityp2,ityp3,iblock), + & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)," ggthet", + & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock), + & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock), + & " ethetai",ethetai + write (iout,*) cosph1ph2(l,k)*sinkt(m), & cosph1ph2(k,l)*sinkt(m), & sinph1ph2(l,k)*sinkt(m),sinph1ph2(k,l)*sinkt(m) @@@ -4976,9 -4928,11 +4976,11 @@@ enddo enddo 10 continue - if (lprn1) write (iout,'(i2,3f8.1,9h ethetai ,f10.5)') - & i,theta(i)*rad2deg,phii*rad2deg, + c lprn1=.true. + if (lprn1) write (iout,'(a4,i2,3f8.1,9h ethetai ,f10.5)') + & 'ebe', i,theta(i)*rad2deg,phii*rad2deg, & phii1*rad2deg,ethetai + c lprn1=.false. etheta=etheta+ethetai if (i.gt.3) gloc(i-3,icg)=gloc(i-3,icg)+wang*dephii if (i.lt.nres) gloc(i-2,icg)=gloc(i-2,icg)+wang*dephii1 @@@ -5319,7 -5273,7 +5321,7 @@@ cosfac=dsqrt(cosfac2) sinfac2=0.5d0/(1.0d0-costtab(i+1)) sinfac=dsqrt(sinfac2) - it=itype(i) + it=iabs(itype(i)) if (it.eq.10) goto 1 c C Compute the axes of tghe local cartesian coordinates system; store in @@@ -5337,7 -5291,7 +5339,7 @@@ C & dc_norm(3,i+nres y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac enddo do j = 1,3 - z_prime(j) = -uz(j,i-1) + z_prime(j) = -uz(j,i-1)*dsign(1.0d0,dfloat(itype(i))) enddo c write (2,*) "i",i c write (2,*) "x_prime",(x_prime(j),j=1,3) @@@ -5369,7 -5323,7 +5371,7 @@@ C Compute the energy of the ith side cbain C c write (2,*) "xx",xx," yy",yy," zz",zz - it=itype(i) + it=iabs(itype(i)) do j = 1,65 x(j) = sc_parmin(j,it) enddo @@@ -5377,7 -5331,7 +5379,7 @@@ Cc diagnostics - remove later xx1 = dcos(alph(2)) yy1 = dsin(alph(2))*dcos(omeg(2)) - zz1 = -dsin(alph(2))*dsin(omeg(2)) + zz1 = -dsign(1.0, dfloat(itype(i)))*dsin(alph(2))*dsin(omeg(2)) write(2,'(3f8.1,3f9.3,1x,3f9.3)') & alph(2)*rad2deg,omeg(2)*rad2deg,theta(3)*rad2deg,xx,yy,zz, & xx1,yy1,zz1 @@@ -5547,10 -5501,8 +5549,10 @@@ c & (dC_norm(j,i-1),j=1,3)," vbld dZZ_Ci1(k)=0.0d0 dZZ_Ci(k)=0.0d0 do j=1,3 - dZZ_Ci(k)=dZZ_Ci(k)-uzgrad(j,k,2,i-1)*dC_norm(j,i+nres) - dZZ_Ci1(k)=dZZ_Ci1(k)-uzgrad(j,k,1,i-1)*dC_norm(j,i+nres) + dZZ_Ci(k)=dZZ_Ci(k)-uzgrad(j,k,2,i-1) + & *dsign(1.0d0,dfloat(itype(i)))*dC_norm(j,i+nres) + dZZ_Ci1(k)=dZZ_Ci1(k)-uzgrad(j,k,1,i-1) + & *dsign(1.0d0,dfloat(itype(i)))*dC_norm(j,i+nres) enddo dXX_XYZ(k)=vbld_inv(i+nres)*(x_prime(k)-xx*dC_norm(k,i+nres)) @@@ -5835,22 -5787,15 +5837,22 @@@ C Set lprn=.true. for debuggin c lprn=.true. etors=0.0D0 do i=iphi_start,iphi_end - etors_ii=0.0D0 + if (itype(i-2).eq.ntyp1 .or. itype(i-1).eq.ntyp1 + & .or. itype(i).eq.ntyp1) cycle + etors_ii=0.0D0 + if (iabs(itype(i)).eq.20) then + iblock=2 + else + iblock=1 + endif itori=itortyp(itype(i-2)) itori1=itortyp(itype(i-1)) phii=phi(i) gloci=0.0D0 C Regular cosine and sine terms - do j=1,nterm(itori,itori1) - v1ij=v1(j,itori,itori1) - v2ij=v2(j,itori,itori1) + do j=1,nterm(itori,itori1,iblock) + v1ij=v1(j,itori,itori1,iblock) + v2ij=v2(j,itori,itori1,iblock) cosphi=dcos(j*phii) sinphi=dsin(j*phii) etors=etors+v1ij*cosphi+v2ij*sinphi @@@ -5865,7 -5810,7 +5867,7 @@@ C [v2 cos(phi/2)+v3 sin(phi/2) C cosphi=dcos(0.5d0*phii) sinphi=dsin(0.5d0*phii) - do j=1,nlor(itori,itori1) + do j=1,nlor(itori,itori1,iblock) vl1ij=vlor1(j,itori,itori1) vl2ij=vlor2(j,itori,itori1) vl3ij=vlor3(j,itori,itori1) @@@ -5878,14 -5823,13 +5880,14 @@@ gloci=gloci+vl1ij*(vl3ij*cosphi-vl2ij*sinphi)*pom enddo C Subtract the constant term - etors=etors-v0(itori,itori1) + etors=etors-v0(itori,itori1,iblock) if (energy_dec) write (iout,'(a6,i5,0pf7.3)') - & 'etor',i,etors_ii-v0(itori,itori1) + & 'etor',i,etors_ii-v0(itori,itori1,iblock) if (lprn) & write (iout,'(2(a3,2x,i3,2x),2i3,6f8.3/26x,6f8.3/)') & restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,itori,itori1, - & (v1(j,itori,itori1),j=1,6),(v2(j,itori,itori1),j=1,6) + & (v1(j,itori,itori1,iblock),j=1,6), + & (v2(j,itori,itori1,iblock),j=1,6) gloc(i-3,icg)=gloc(i-3,icg)+wtor*gloci c write (iout,*) 'i=',i,' gloc=',gloc(i-3,icg) enddo @@@ -5936,10 -5880,7 +5938,10 @@@ C Set lprn=.true. for debuggin lprn=.false. c lprn=.true. etors_d=0.0D0 +c write(iout,*) "a tu??" do i=iphid_start,iphid_end + if (itype(i-2).eq.ntyp1 .or. itype(i-1).eq.ntyp1 + & .or. itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle itori=itortyp(itype(i-2)) itori1=itortyp(itype(i-1)) itori2=itortyp(itype(i)) @@@ -5947,15 -5888,11 +5949,15 @@@ phii1=phi(i+1) gloci1=0.0D0 gloci2=0.0D0 - do j=1,ntermd_1(itori,itori1,itori2) - v1cij=v1c(1,j,itori,itori1,itori2) - v1sij=v1s(1,j,itori,itori1,itori2) - v2cij=v1c(2,j,itori,itori1,itori2) - v2sij=v1s(2,j,itori,itori1,itori2) + iblock=1 + if (iabs(itype(i+1)).eq.20) iblock=2 + +C Regular cosine and sine terms + do j=1,ntermd_1(itori,itori1,itori2,iblock) + v1cij=v1c(1,j,itori,itori1,itori2,iblock) + v1sij=v1s(1,j,itori,itori1,itori2,iblock) + v2cij=v1c(2,j,itori,itori1,itori2,iblock) + v2sij=v1s(2,j,itori,itori1,itori2,iblock) cosphi1=dcos(j*phii) sinphi1=dsin(j*phii) cosphi2=dcos(j*phii1) @@@ -5965,12 -5902,12 +5967,12 @@@ gloci1=gloci1+j*(v1sij*cosphi1-v1cij*sinphi1) gloci2=gloci2+j*(v2sij*cosphi2-v2cij*sinphi2) enddo - do k=2,ntermd_2(itori,itori1,itori2) + do k=2,ntermd_2(itori,itori1,itori2,iblock) do l=1,k-1 - v1cdij = v2c(k,l,itori,itori1,itori2) - v2cdij = v2c(l,k,itori,itori1,itori2) - v1sdij = v2s(k,l,itori,itori1,itori2) - v2sdij = v2s(l,k,itori,itori1,itori2) + v1cdij = v2c(k,l,itori,itori1,itori2,iblock) + v2cdij = v2c(l,k,itori,itori1,itori2,iblock) + v1sdij = v2s(k,l,itori,itori1,itori2,iblock) + v2sdij = v2s(l,k,itori,itori1,itori2,iblock) cosphi1p2=dcos(l*phii+(k-l)*phii1) cosphi1m2=dcos(l*phii-(k-l)*phii1) sinphi1p2=dsin(l*phii+(k-l)*phii1) @@@ -5985,6 -5922,7 +5987,6 @@@ enddo gloc(i-3,icg)=gloc(i-3,icg)+wtor_d*gloci1 gloc(i-2,icg)=gloc(i-2,icg)+wtor_d*gloci2 -c write (iout,*) "gloci", gloc(i-3,icg) enddo return end @@@ -6015,11 -5953,10 +6017,11 @@@ c amino-acid residues C Set lprn=.true. for debugging lprn=.false. c lprn=.true. -c write (iout,*) "EBACK_SC_COR",iphi_start,iphi_end,nterm_sccor +c write (iout,*) "EBACK_SC_COR",itau_start,itau_end esccor=0.0D0 do i=itau_start,itau_end esccor_ii=0.0D0 + if ((itype(i-2).eq.ntyp1).or.(itype(i-1).eq.ntyp1)) cycle isccori=isccortyp(itype(i-2)) isccori1=isccortyp(itype(i-1)) phii=phi(i) @@@ -6038,16 -5975,14 +6040,16 @@@ c 2 = Ca...Ca...Ca...S c 3 = SC...Ca...Ca...SCi gloci=0.0D0 if (((intertyp.eq.3).and.((itype(i-2).eq.10).or. - & (itype(i-1).eq.10).or.(itype(i-2).eq.21).or. - & (itype(i-1).eq.21))) + & (itype(i-1).eq.10).or.(itype(i-2).eq.ntyp1).or. + & (itype(i-1).eq.ntyp1))) & .or. ((intertyp.eq.1).and.((itype(i-2).eq.10) - & .or.(itype(i-2).eq.21))) + & .or.(itype(i-2).eq.ntyp1).or.(itype(i-1).eq.ntyp1) + & .or.(itype(i).eq.ntyp1))) & .or.((intertyp.eq.2).and.((itype(i-1).eq.10).or. - & (itype(i-1).eq.21)))) cycle - if ((intertyp.eq.2).and.(i.eq.4).and.(itype(1).eq.21)) cycle - if ((intertyp.eq.1).and.(i.eq.nres).and.(itype(nres).eq.21)) + & (itype(i-1).eq.ntyp1).or.(itype(i-2).eq.ntyp1).or. + & (itype(i-3).eq.ntyp1)))) cycle + if ((intertyp.eq.2).and.(i.eq.4).and.(itype(1).eq.ntyp1)) cycle + if ((intertyp.eq.1).and.(i.eq.nres).and.(itype(nres).eq.ntyp1)) & cycle do j=1,nterm_sccor(isccori,isccori1) v1ij=v1sccor(j,intertyp,isccori,isccori1) @@@ -6062,9 -5997,9 +6064,9 @@@ c write (iout,*) "WTF",intertyp, c &gloc_sc(intertyp,i-3,icg) if (lprn) & write (iout,'(2(a3,2x,i3,2x),2i3,6f8.3/26x,6f8.3/)') - & restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,itori,itori1, - & (v1sccor(j,intertyp,itori,itori1),j=1,6) - & ,(v2sccor(j,intertyp,itori,itori1),j=1,6) + & restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,isccori,isccori1, + & (v1sccor(j,intertyp,isccori,isccori1),j=1,6) + & ,(v2sccor(j,intertyp,isccori,isccori1),j=1,6) gsccor_loc(i-3)=gsccor_loc(i-3)+gloci enddo !intertyp enddo diff --combined source/unres/src_MIN/CMakeLists.txt index 3d930f7,ed0bb6e..5d8442f --- a/source/unres/src_MIN/CMakeLists.txt +++ b/source/unres/src_MIN/CMakeLists.txt @@@ -33,7 -33,6 +33,7 @@@ set(UNRES_MIN_SRC printmat.f randgens.f readrtns_min.F + refsys.f rescode.f refsys.f rmdd.f @@@ -209,41 -208,17 +209,17 @@@ set(UNRES_MIN_SRCS ${UNRES_MIN_SRC0} ${ #========================================= # Build the binary #========================================= - add_executable(UNRES_BIN-MIN ${UNRES_MIN_SRCS} ) - set_target_properties(UNRES_BIN-MIN PROPERTIES OUTPUT_NAME ${UNRES_BIN}) + add_executable(UNRES_MIN_BIN ${UNRES_MIN_SRCS} ) + set_target_properties(UNRES_MIN_BIN PROPERTIES OUTPUT_NAME ${UNRES_BIN}) if (Fortran_COMPILER_NAME STREQUAL "ifort") - target_link_libraries (UNRES_BIN-MIN ${CMAKE_THREAD_LIBS_INIT}) + target_link_libraries (UNRES_MIN_BIN ${CMAKE_THREAD_LIBS_INIT}) endif (Fortran_COMPILER_NAME STREQUAL "ifort") + set_property(TARGET UNRES_MIN_BIN PROPERTY RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin ) - #set_property(TARGET ${UNRES_BIN} PROPERTY RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin/unres/MD ) #========================================= - # TESTS + # Install Path #========================================= + install(TARGETS UNRES_MIN_BIN DESTINATION ${CMAKE_INSTALL_PREFIX}) - #-- Copy all the data files from the test directory into the source directory - #SET(UNRES_TEST_FILES - # ala10.inp - # ) - - #FOREACH (UNRES_TEST_FILE ${UNRES_TEST_FILES}) - # SET (unres_test_dest "${CMAKE_CURRENT_BINARY_DIR}/${UNRES_TEST_FILE}") - # MESSAGE (STATUS " Copying ${UNRES_TEST_FILE} from ${CMAKE_SOURCE_DIR}/examples/unres/MD/ff_gab/${UNRES_TEST_FILE} to ${unres_test_dest}") - # ADD_CUSTOM_COMMAND ( - # TARGET ${UNRES_BIN} - # POST_BUILD - # COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_SOURCE_DIR}/examples/unres/MD/ff_gab/${UNRES_TEST_FILE} ${unres_test_dest} - # ) - #ENDFOREACH (UNRES_TEST_FILE ${UNRES_TEST_FILES}) - - #========================================= - # Generate data test files - #========================================= - - #if(NOT UNRES_WITH_MPI) - - # add_test(NAME UNRES_MD_Ala10 COMMAND sh ${CMAKE_CURRENT_BINARY_DIR}/test_single_ala.sh ) - - #endif(NOT UNRES_WITH_MPI) - diff --combined source/wham/src-M/CMakeLists.txt index 2576a15,afa0f19..312fb87 --- a/source/wham/src-M/CMakeLists.txt +++ b/source/wham/src-M/CMakeLists.txt @@@ -96,9 -96,11 +96,11 @@@ set(UNRES_WHAM_M_PP_SR # Set comipiler flags for different sourcefiles #================================================ if (Fortran_COMPILER_NAME STREQUAL "ifort") - set(FFLAGS0 "-g -CB -I. -I${CMAKE_CURRENT_SOURCE_DIR}/include_unres -I${MPIF_INCLUDE_DIRECTORIES}" ) + set(FFLAGS0 "-g -CB -I. -I${CMAKE_CURRENT_SOURCE_DIR}/include_unres" ) elseif (Fortran_COMPILER_NAME STREQUAL "gfortran") - set(FFLAGS0 "-std=legacy -g -I. -I${CMAKE_CURRENT_SOURCE_DIR}/include_unres -I${MPIF_INCLUDE_DIRECTORIES}" ) + set(FFLAGS0 "-std=legacy -g -I. -I${CMAKE_CURRENT_SOURCE_DIR}/include_unres" ) + else () + set(FFLAGS0 "-g -I. -I${CMAKE_CURRENT_SOURCE_DIR}/include_unres" ) endif (Fortran_COMPILER_NAME STREQUAL "ifort") @@@ -106,7 -108,7 +108,7 @@@ # Add MPI compiler flags #========================================= if(UNRES_WITH_MPI) - set(FFLAGS0 "${FFLAGS0} -I${MPIF_INCLUDE_DIRECTORIES}") + set(FFLAGS0 "${FFLAGS0} -I${MPI_Fortran_INCLUDE_PATH}") endif(UNRES_WITH_MPI) set_property(SOURCE ${UNRES_WHAM_M_SRC0} PROPERTY COMPILE_FLAGS ${FFLAGS0} ) @@@ -118,7 -120,6 +120,7 @@@ if(UNRES_MD_FF STREQUAL "GAB" # set preprocesor flags set(CPPFLAGS "PROCOR -DSPLITELE -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -DSCCORPDB" ) + #========================================= # Settings for E0LL2Y force field #========================================= @@@ -152,9 -153,6 +154,9 @@@ elseif (Fortran_COMPILER_NAME STREQUAL elseif (Fortran_COMPILER_NAME STREQUAL "gfortran") # Add old gfortran flags set(CPPFLAGS "${CPPFLAGS} -DG77") +else (Fortran_COMPILER_NAME STREQUAL "ifort") + # Default preprocessor flags + set(CPPFLAGS "${CPPFLAGS} -DPGI") endif (Fortran_COMPILER_NAME STREQUAL "ifort") #========================================= @@@ -178,7 -176,7 +180,7 @@@ set_property(SOURCE ${UNRES_WHAM_M_PP_S #======================================== # Setting binary name #======================================== - set(UNRES_WHAM_M_BIN "wham_${Fortran_COMPILER_NAME}.exe") + set(UNRES_WHAM_M_BIN "wham_M_${Fortran_COMPILER_NAME}.exe") #========================================= # cinfo.f workaround for CMake @@@ -222,18 -220,24 +224,24 @@@ set(UNRES_WHAM_M_SRCS ${UNRES_WHAM_M_SR #========================================= add_executable(UNRES_WHAM_M_BIN ${UNRES_WHAM_M_SRCS} ) set_target_properties(UNRES_WHAM_M_BIN PROPERTIES OUTPUT_NAME ${UNRES_WHAM_M_BIN}) - - #set_property(TARGET ${UNRES_BIN} PROPERTY RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin/unres/MD ) + set_property(TARGET UNRES_WHAM_M_BIN PROPERTY RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin ) #add_dependencies (${UNRES_BIN} ${UNRES_XDRFLIB}) #========================================= # Link libraries #========================================= # link MPI library (libmpich.a) - target_link_libraries( UNRES_WHAM_M_BIN ${MPIF_LIBRARIES} ) + target_link_libraries( UNRES_WHAM_M_BIN ${MPI_Fortran_LIBRARIES} ) # link libxdrf.a target_link_libraries( UNRES_WHAM_M_BIN xdrf ) + + #========================================= + # Install Path + #========================================= + install(TARGETS UNRES_WHAM_M_BIN DESTINATION ${CMAKE_INSTALL_PREFIX}) + + #========================================= # TESTS #========================================= diff --combined source/wham/src/CMakeLists.txt index 556250e,e7f990e..d441588 --- a/source/wham/src/CMakeLists.txt +++ b/source/wham/src/CMakeLists.txt @@@ -94,9 -94,11 +94,11 @@@ set(UNRES_WHAM_PP_SR # Set comipiler flags for different sourcefiles #================================================ if (Fortran_COMPILER_NAME STREQUAL "ifort") - set(FFLAGS0 "-mcmodel=medium -g -CB -I. -I${CMAKE_CURRENT_SOURCE_DIR}/include_unres" ) + set(FFLAGS0 "-mcmodel=large -g -CB -I. -I${CMAKE_CURRENT_SOURCE_DIR}/include_unres" ) elseif (Fortran_COMPILER_NAME STREQUAL "gfortran") set(FFLAGS0 "-std=legacy -g -I. -I${CMAKE_CURRENT_SOURCE_DIR}/include_unres" ) + else () + set(FFLAGS0 "-g -I. -I${CMAKE_CURRENT_SOURCE_DIR}/include_unres" ) endif (Fortran_COMPILER_NAME STREQUAL "ifort") @@@ -104,7 -106,7 +106,7 @@@ # Add MPI compiler flags #========================================= if(UNRES_WITH_MPI) - set(FFLAGS0 "${FFLAGS0} -I${MPIF_INCLUDE_DIRECTORIES}") + set(FFLAGS0 "${FFLAGS0} -I${MPI_Fortran_INCLUDE_PATH}") endif(UNRES_WITH_MPI) set_property(SOURCE ${UNRES_WHAM_SRC0} PROPERTY COMPILE_FLAGS ${FFLAGS0} ) @@@ -152,9 -154,6 +154,9 @@@ elseif (Fortran_COMPILER_NAME STREQUAL elseif (Fortran_COMPILER_NAME STREQUAL "gfortran") # Add old gfortran flags set(CPPFLAGS "${CPPFLAGS} -DG77") +else (Fortran_COMPILER_NAME STREQUAL "ifort") + # Default preprocessor flags + set(CPPFLAGS "${CPPFLAGS} -DPGI") endif (Fortran_COMPILER_NAME STREQUAL "ifort") #========================================= @@@ -222,19 -221,24 +224,24 @@@ set(UNRES_WHAM_SRCS ${UNRES_WHAM_SRC0} #========================================= add_executable(UNRES_WHAM_BIN ${UNRES_WHAM_SRCS} ) set_target_properties(UNRES_WHAM_BIN PROPERTIES OUTPUT_NAME ${UNRES_WHAM_BIN}) - - #set_property(TARGET ${UNRES_BIN} PROPERTY RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin/unres/MD ) + set_property(TARGET UNRES_WHAM_BIN PROPERTY RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin ) #add_dependencies (${UNRES_BIN} ${UNRES_XDRFLIB}) #========================================= # Link libraries #========================================= - # link MPI library (libmpich.a) - target_link_libraries( UNRES_WHAM_BIN ${MPIF_LIBRARIES} ) + # link MPI libraries + target_link_libraries( UNRES_WHAM_BIN ${MPI_Fortran_LIBRARIES} ) # link libxdrf.a target_link_libraries( UNRES_WHAM_BIN xdrf ) #========================================= + # Install Path + #========================================= + install(TARGETS UNRES_WHAM_BIN DESTINATION ${CMAKE_INSTALL_PREFIX}) + + + #========================================= # TESTS #========================================= diff --combined source/wham/src/energy_p_new.F index a53e6e9,13fe796..7244671 --- a/source/wham/src/energy_p_new.F +++ b/source/wham/src/energy_p_new.F @@@ -229,7 -229,7 +229,7 @@@ & +wturn3*fact(2)*gel_loc_turn3(i) & +wturn6*fact(5)*gel_loc_turn6(i) & +wel_loc*fact(2)*gel_loc_loc(i) - & +wsccor*fact(1)*gsccor_loc(i) +c & +wsccor*fact(1)*gsccor_loc(i) enddo endif return @@@ -369,9 -369,8 +369,9 @@@ cd print *,'Entering ELJ nnt=',nnt, evdw=0.0D0 evdw_t=0.0d0 do i=iatsc_s,iatsc_e - itypi=itype(i) - itypi1=itype(i+1) + itypi=iabs(itype(i)) + if (itypi.eq.ntyp1) cycle + itypi1=iabs(itype(i+1)) xi=c(1,nres+i) yi=c(2,nres+i) zi=c(3,nres+i) @@@ -384,8 -383,7 +384,8 @@@ cd write (iout,*) 'i=',i,' iint=',iint,' istart=',istart(i,iint), cd & 'iend=',iend(i,iint) do j=istart(i,iint),iend(i,iint) - itypj=itype(j) + itypj=iabs(itype(j)) + if (itypj.eq.ntyp1) cycle xj=c(1,nres+j)-xi yj=c(2,nres+j)-yi zj=c(3,nres+j)-zi @@@ -542,9 -540,8 +542,9 @@@ c print *,'Entering ELJK nnt=',nnt, evdw=0.0D0 evdw_t=0.0d0 do i=iatsc_s,iatsc_e - itypi=itype(i) - itypi1=itype(i+1) + itypi=iabs(itype(i)) + if (itypi.eq.ntyp1) cycle + itypi1=iabs(itype(i+1)) xi=c(1,nres+i) yi=c(2,nres+i) zi=c(3,nres+i) @@@ -553,8 -550,7 +553,8 @@@ C Calculate SC interaction energy C do iint=1,nint_gr(i) do j=istart(i,iint),iend(i,iint) - itypj=itype(j) + itypj=iabs(itype(j)) + if (itypj.eq.ntyp1) cycle xj=c(1,nres+j)-xi yj=c(2,nres+j)-yi zj=c(3,nres+j)-zi @@@ -655,8 -651,8 +655,8 @@@ c els c endif ind=0 do i=iatsc_s,iatsc_e - itypi=itype(i) - itypi1=itype(i+1) + itypi=iabs(itype(i)) + itypi1=iabs(itype(i+1)) xi=c(1,nres+i) yi=c(2,nres+i) zi=c(3,nres+i) @@@ -670,7 -666,7 +670,7 @@@ do iint=1,nint_gr(i) do j=istart(i,iint),iend(i,iint) ind=ind+1 - itypj=itype(j) + itypj=iabs(itype(j)) dscj_inv=vbld_inv(j+nres) chi1=chi(itypi,itypj) chi2=chi(itypj,itypi) @@@ -792,8 -788,8 +792,8 @@@ c print *,'Entering EGB nnt=',nnt, c if (icall.gt.0) lprn=.true. ind=0 do i=iatsc_s,iatsc_e - itypi=itype(i) - itypi1=itype(i+1) + itypi=iabs(itype(i)) + itypi1=iabs(itype(i+1)) xi=c(1,nres+i) yi=c(2,nres+i) zi=c(3,nres+i) @@@ -822,7 -818,7 +822,7 @@@ c if (energy_dec) write (i c & 'evdw',i,j,evdwij,' ss' ELSE ind=ind+1 - itypj=itype(j) + itypj=iabs(itype(j)) dscj_inv=vbld_inv(j+nres) sig0ij=sigma(itypi,itypj) chi1=chi(itypi,itypj) @@@ -954,8 -950,8 +954,8 @@@ c print *,'Entering EGB nnt=',nnt, c if (icall.gt.0) lprn=.true. ind=0 do i=iatsc_s,iatsc_e - itypi=itype(i) - itypi1=itype(i+1) + itypi=iabs(itype(i)) + itypi1=iabs(itype(i+1)) xi=c(1,nres+i) yi=c(2,nres+i) zi=c(3,nres+i) @@@ -969,7 -965,7 +969,7 @@@ do iint=1,nint_gr(i) do j=istart(i,iint),iend(i,iint) ind=ind+1 - itypj=itype(j) + itypj=iabs(itype(j)) dscj_inv=vbld_inv(j+nres) sig0ij=sigma(itypi,itypj) r0ij=r0(itypi,itypj) @@@ -2808,7 -2804,7 +2808,7 @@@ c & " iscp",(iscpstart(i,j),iscpe do iint=1,nscp_gr(i) do j=iscpstart(i,iint),iscpend(i,iint) - itypj=itype(j) + itypj=iabs(itype(j)) C Uncomment following three lines for SC-p interactions c xj=c(1,nres+j)-xi c yj=c(2,nres+j)-yi @@@ -2922,8 -2918,7 +2922,8 @@@ C 24/11/03 AL: SS bridges handled separ C distance and angle dependent SS bond potential. if (.not.dyn_ss .and. i.le.nss) then C 15/02/13 CC dynamic SSbond - additional check - if (ii.gt.nres .and. itype(iii).eq.1 .and. itype(jjj).eq.1) then + if (ii.gt.nres .and. iabs(itype(iii)).eq.1 .and. + & iabs(itype(jjj)).eq.1) then call ssbond_ene(iii,jjj,eij) ehpb=ehpb+2*eij endif @@@ -3024,7 -3019,7 +3024,7 @@@ include 'COMMON.VAR' include 'COMMON.IOUNITS' double precision erij(3),dcosom1(3),dcosom2(3),gg(3) - itypi=itype(i) + itypi=iabs(itype(i)) xi=c(1,nres+i) yi=c(2,nres+i) zi=c(3,nres+i) @@@ -3032,7 -3027,7 +3032,7 @@@ dyi=dc_norm(2,nres+i) dzi=dc_norm(3,nres+i) dsci_inv=dsc_inv(itypi) - itypj=itype(j) + itypj=iabs(itype(j)) dscj_inv=dsc_inv(itypj) xj=c(1,nres+j)-xi yj=c(2,nres+j)-yi @@@ -3124,7 -3119,7 +3124,7 @@@ c 09/18/07 AL: multimodal bond potential based on AM1 CA-SC PMF's included c do i=nnt,nct - iti=itype(i) + iti=iabs(itype(i)) if (iti.ne.10) then nbi=nbondterm(iti) if (nbi.eq.1) then @@@ -3206,18 -3201,6 +3206,18 @@@ c write (iout,*) ithet_start,ithet C Zero the energy function and its derivative at 0 or pi. call splinthet(theta(i),0.5d0*delta,ss,ssd) it=itype(i-1) + ichir1=isign(1,itype(i-2)) + ichir2=isign(1,itype(i)) + if (itype(i-2).eq.10) ichir1=isign(1,itype(i-1)) + if (itype(i).eq.10) ichir2=isign(1,itype(i-1)) + if (itype(i-1).eq.10) then + itype1=isign(10,itype(i-2)) + ichir11=isign(1,itype(i-2)) + ichir12=isign(1,itype(i-2)) + itype2=isign(10,itype(i)) + ichir21=isign(1,itype(i)) + ichir22=isign(1,itype(i)) + endif c if (i.gt.ithet_start .and. c & (itel(i-1).eq.0 .or. itel(i-2).eq.0)) goto 1215 c if (i.gt.3 .and. (i.le.4 .or. itel(i-3).ne.0)) then @@@ -3273,12 -3256,8 +3273,12 @@@ C dependent on the adjacent virtual-bon C In following comments this theta will be referred to as t_c. thet_pred_mean=0.0d0 do k=1,2 - athetk=athet(k,it) - bthetk=bthet(k,it) + athetk=athet(k,it,ichir1,ichir2) + bthetk=bthet(k,it,ichir1,ichir2) + if (it.eq.10) then + athetk=athet(k,itype1,ichir11,ichir12) + bthetk=bthet(k,itype2,ichir21,ichir22) + endif thet_pred_mean=thet_pred_mean+athetk*y(k)+bthetk*z(k) enddo c write (iout,*) "thet_pred_mean",thet_pred_mean @@@ -3286,16 -3265,8 +3286,16 @@@ thet_pred_mean=thet_pred_mean*ss+a0thet(it) c write (iout,*) "thet_pred_mean",thet_pred_mean C Derivatives of the "mean" values in gamma1 and gamma2. - dthetg1=(-athet(1,it)*y(2)+athet(2,it)*y(1))*ss - dthetg2=(-bthet(1,it)*z(2)+bthet(2,it)*z(1))*ss + dthetg1=(-athet(1,it,ichir1,ichir2)*y(2) + &+athet(2,it,ichir1,ichir2)*y(1))*ss + dthetg2=(-bthet(1,it,ichir1,ichir2)*z(2) + & +bthet(2,it,ichir1,ichir2)*z(1))*ss + if (it.eq.10) then + dthetg1=(-athet(1,itype1,ichir11,ichir12)*y(2) + &+athet(2,itype1,ichir11,ichir12)*y(1))*ss + dthetg2=(-bthet(1,itype2,ichir21,ichir22)*z(2) + & +bthet(2,itype2,ichir21,ichir22)*z(1))*ss + endif if (theta(i).gt.pi-delta) then call theteng(pi-delta,thet_pred_mean,theta0(it),f0,fprim0, & E_tc0) @@@ -3466,13 -3437,11 +3466,13 @@@ etheta=0.0D0 c write (iout,*) "ithetyp",(ithetyp(i),i=1,ntyp1) do i=ithet_start,ithet_end + if (iabs(itype(i+1)).eq.20) iblock=2 + if (iabs(itype(i+1)).ne.20) iblock=1 dethetai=0.0d0 dephii=0.0d0 dephii1=0.0d0 theti2=0.5d0*theta(i) - ityp2=ithetyp(itype(i-1)) + ityp2=ithetyp((itype(i-1))) do k=1,nntheterm coskt(k)=dcos(k*theti2) sinkt(k)=dsin(k*theti2) @@@ -3484,7 -3453,7 +3484,7 @@@ #else phii=phi(i) #endif - ityp1=ithetyp(itype(i-2)) + ityp1=ithetyp(iabs(itype(i-2))) do k=1,nsingle cosph1(k)=dcos(k*phii) sinph1(k)=dsin(k*phii) @@@ -3505,7 -3474,7 +3505,7 @@@ #else phii1=phi(i+1) #endif - ityp3=ithetyp(itype(i)) + ityp3=ithetyp((itype(i))) do k=1,nsingle cosph2(k)=dcos(k*phii1) sinph2(k)=dsin(k*phii1) @@@ -3521,7 -3490,7 +3521,7 @@@ c write (iout,*) "i",i," ityp1",itype(i-2),ityp1, c & " ityp2",itype(i-1),ityp2," ityp3",itype(i),ityp3 c call flush(iout) - ethetai=aa0thet(ityp1,ityp2,ityp3) + ethetai=aa0thet(ityp1,ityp2,ityp3,iblock) do k=1,ndouble do l=1,k-1 ccl=cosph1(l)*cosph2(k-l) @@@ -3543,12 -3512,11 +3543,12 @@@ enddo endif do k=1,ntheterm - ethetai=ethetai+aathet(k,ityp1,ityp2,ityp3)*sinkt(k) - dethetai=dethetai+0.5d0*k*aathet(k,ityp1,ityp2,ityp3) + ethetai=ethetai+aathet(k,ityp1,ityp2,ityp3,iblock)*sinkt(k) + dethetai=dethetai+0.5d0*k*aathet(k,ityp1,ityp2,ityp3,iblock) & *coskt(k) if (lprn) - & write (iout,*) "k",k," aathet",aathet(k,ityp1,ityp2,ityp3), + & write (iout,*) "k",k," aathet",aathet(k,ityp1,ityp2,ityp3, + & iblock), & " ethetai",ethetai enddo if (lprn) then @@@ -3567,24 -3535,24 +3567,24 @@@ endif do m=1,ntheterm2 do k=1,nsingle - aux=bbthet(k,m,ityp1,ityp2,ityp3)*cosph1(k) - & +ccthet(k,m,ityp1,ityp2,ityp3)*sinph1(k) - & +ddthet(k,m,ityp1,ityp2,ityp3)*cosph2(k) - & +eethet(k,m,ityp1,ityp2,ityp3)*sinph2(k) + aux=bbthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph1(k) + & +ccthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph1(k) + & +ddthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph2(k) + & +eethet(k,m,ityp1,ityp2,ityp3,iblock)*sinph2(k) ethetai=ethetai+sinkt(m)*aux dethetai=dethetai+0.5d0*m*aux*coskt(m) dephii=dephii+k*sinkt(m)*( - & ccthet(k,m,ityp1,ityp2,ityp3)*cosph1(k)- - & bbthet(k,m,ityp1,ityp2,ityp3)*sinph1(k)) + & ccthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph1(k)- + & bbthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph1(k)) dephii1=dephii1+k*sinkt(m)*( - & eethet(k,m,ityp1,ityp2,ityp3)*cosph2(k)- - & ddthet(k,m,ityp1,ityp2,ityp3)*sinph2(k)) + & eethet(k,m,ityp1,ityp2,ityp3,iblock)*cosph2(k)- + & ddthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph2(k)) if (lprn) & write (iout,*) "m",m," k",k," bbthet", - & bbthet(k,m,ityp1,ityp2,ityp3)," ccthet", - & ccthet(k,m,ityp1,ityp2,ityp3)," ddthet", - & ddthet(k,m,ityp1,ityp2,ityp3)," eethet", - & eethet(k,m,ityp1,ityp2,ityp3)," ethetai",ethetai + & bbthet(k,m,ityp1,ityp2,ityp3,iblock)," ccthet", + & ccthet(k,m,ityp1,ityp2,ityp3,iblock)," ddthet", + & ddthet(k,m,ityp1,ityp2,ityp3,iblock)," eethet", + & eethet(k,m,ityp1,ityp2,ityp3,iblock)," ethetai",ethetai enddo enddo if (lprn) @@@ -3592,29 -3560,28 +3592,29 @@@ do m=1,ntheterm3 do k=2,ndouble do l=1,k-1 - aux=ffthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)+ - & ffthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l)+ - & ggthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)+ - & ggthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l) + aux=ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)+ + & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l)+ + & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)+ + & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l) ethetai=ethetai+sinkt(m)*aux dethetai=dethetai+0.5d0*m*coskt(m)*aux dephii=dephii+l*sinkt(m)*( - & -ffthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)- - & ffthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)+ - & ggthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)+ - & ggthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l)) + & -ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)- + & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l)+ + & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)+ + & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l)) dephii1=dephii1+(k-l)*sinkt(m)*( - & -ffthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)+ - & ffthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)+ - & ggthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)- - & ggthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l)) + & -ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)+ + & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l)+ + & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)- + & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l)) if (lprn) then write (iout,*) "m",m," k",k," l",l," ffthet", - & ffthet(l,k,m,ityp1,ityp2,ityp3), - & ffthet(k,l,m,ityp1,ityp2,ityp3)," ggthet", - & ggthet(l,k,m,ityp1,ityp2,ityp3), - & ggthet(k,l,m,ityp1,ityp2,ityp3)," ethetai",ethetai + & ffthet(l,k,m,ityp1,ityp2,ityp3,iblock), + & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)," ggthet", + & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock), + & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)," ethetai", + & ethetai write (iout,*) cosph1ph2(l,k)*sinkt(m), & cosph1ph2(k,l)*sinkt(m), & sinph1ph2(l,k)*sinkt(m),sinph1ph2(k,l)*sinkt(m) @@@ -3623,10 -3590,13 +3623,13 @@@ enddo enddo 10 continue - if (lprn1) write (iout,'(i2,3f8.1,9h ethetai ,f10.5)') - & i,theta(i)*rad2deg,phii*rad2deg, + c lprn1=.true. + if (lprn1) write (iout,'(a4,i2,3f8.1,9h ethetai ,f10.5)') + & 'ebe',i,theta(i)*rad2deg,phii*rad2deg, & phii1*rad2deg,ethetai + c lprn1=.false. etheta=etheta+ethetai + if (i.gt.3) gloc(i-3,icg)=gloc(i-3,icg)+wang*dephii if (i.lt.nres) gloc(i-2,icg)=gloc(i-2,icg)+wang*dephii1 gloc(nphi+i-2,icg)=wang*dethetai @@@ -3661,7 -3631,7 +3664,7 @@@ c write (iout,'(a)') 'ESC do i=loc_start,loc_end it=itype(i) if (it.eq.10) goto 1 - nlobit=nlob(it) + nlobit=nlob(iabs(it)) c print *,'i=',i,' it=',it,' nlobit=',nlobit c write (iout,*) 'i=',i,' ssa=',ssa,' ssad=',ssad theti=theta(i+1)-pipol @@@ -3816,7 -3786,7 +3819,7 @@@ C Compute the contribution to SC energ do iii=-1,1 do j=1,nlobit - expfac=dexp(bsc(j,it)-0.5D0*contr(j,iii)+emin) + expfac=dexp(bsc(j,iabs(it))-0.5D0*contr(j,iii)+emin) cd print *,'j=',j,' expfac=',expfac escloc_i=escloc_i+expfac do k=1,3 @@@ -3897,7 -3867,7 +3900,7 @@@ C Compute the contribution to SC energ dersc12=0.0d0 do j=1,nlobit - expfac=dexp(bsc(j,it)-0.5D0*contr(j)+emin) + expfac=dexp(bsc(j,iabs(it))-0.5D0*contr(j)+emin) escloc_i=escloc_i+expfac do k=1,2 dersc(k)=dersc(k)+Ax(k,j)*expfac @@@ -3960,7 -3930,7 +3963,7 @@@ cosfac=dsqrt(cosfac2) sinfac2=0.5d0/(1.0d0-costtab(i+1)) sinfac=dsqrt(sinfac2) - it=itype(i) + it=iabs(itype(i)) if (it.eq.10) goto 1 c C Compute the axes of tghe local cartesian coordinates system; store in @@@ -3978,7 -3948,7 +3981,7 @@@ C & dc_norm(3,i+nres y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac enddo do j = 1,3 - z_prime(j) = -uz(j,i-1) + z_prime(j) = -uz(j,i-1)*dsign(1.0d0,dfloat(itype(i))) enddo c write (2,*) "i",i c write (2,*) "x_prime",(x_prime(j),j=1,3) @@@ -4010,7 -3980,7 +4013,7 @@@ C Compute the energy of the ith side cbain C c write (2,*) "xx",xx," yy",yy," zz",zz - it=itype(i) + it=iabs(itype(i)) do j = 1,65 x(j) = sc_parmin(j,it) enddo @@@ -4018,7 -3988,7 +4021,7 @@@ Cc diagnostics - remove later xx1 = dcos(alph(2)) yy1 = dsin(alph(2))*dcos(omeg(2)) - zz1 = -dsin(alph(2))*dsin(omeg(2)) + zz1 = -dsign(1.0d0,itype(i))*dsin(alph(2))*dsin(omeg(2)) write(2,'(3f8.1,3f9.3,1x,3f9.3)') & alph(2)*rad2deg,omeg(2)*rad2deg,theta(3)*rad2deg,xx,yy,zz, & xx1,yy1,zz1 @@@ -4190,11 -4160,8 +4193,11 @@@ c & (dC_norm(j,i-1),j=1,3)," vbld dZZ_Ci1(k)=0.0d0 dZZ_Ci(k)=0.0d0 do j=1,3 - dZZ_Ci(k)=dZZ_Ci(k)-uzgrad(j,k,2,i-1)*dC_norm(j,i+nres) - dZZ_Ci1(k)=dZZ_Ci1(k)-uzgrad(j,k,1,i-1)*dC_norm(j,i+nres) + dZZ_Ci(k)=dZZ_Ci(k)-uzgrad(j,k,2,i-1) + & *dsign(1.0d0,dfloat(itype(i)))*dC_norm(j,i+nres) + dZZ_Ci1(k)=dZZ_Ci1(k)-uzgrad(j,k,1,i-1) + & *dsign(1.0d0,dfloat(itype(i)))*dC_norm(j,i+nres) + enddo dXX_XYZ(k)=vbld_inv(i+nres)*(x_prime(k)-xx*dC_norm(k,i+nres)) @@@ -4430,19 -4397,14 +4433,19 @@@ c lprn=.true etors=0.0D0 do i=iphi_start,iphi_end if (itel(i-2).eq.0 .or. itel(i-1).eq.0) goto 1215 + if (iabs(itype(i)).eq.20) then + iblock=2 + else + iblock=1 + endif itori=itortyp(itype(i-2)) itori1=itortyp(itype(i-1)) phii=phi(i) gloci=0.0D0 C Regular cosine and sine terms - do j=1,nterm(itori,itori1) - v1ij=v1(j,itori,itori1) - v2ij=v2(j,itori,itori1) + do j=1,nterm(itori,itori1,iblock) + v1ij=v1(j,itori,itori1,iblock) + v2ij=v2(j,itori,itori1,iblock) cosphi=dcos(j*phii) sinphi=dsin(j*phii) etors=etors+v1ij*cosphi+v2ij*sinphi @@@ -4455,7 -4417,7 +4458,7 @@@ C [v2 cos(phi/2)+v3 sin(phi/2) C cosphi=dcos(0.5d0*phii) sinphi=dsin(0.5d0*phii) - do j=1,nlor(itori,itori1) + do j=1,nlor(itori,itori1,iblock) vl1ij=vlor1(j,itori,itori1) vl2ij=vlor2(j,itori,itori1) vl3ij=vlor3(j,itori,itori1) @@@ -4466,11 -4428,11 +4469,11 @@@ gloci=gloci+vl1ij*(vl3ij*cosphi-vl2ij*sinphi)*pom enddo C Subtract the constant term - etors=etors-v0(itori,itori1) + etors=etors-v0(itori,itori1,iblock) if (lprn) & write (iout,'(2(a3,2x,i3,2x),2i3,6f8.3/26x,6f8.3/)') & restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,itori,itori1, - & (v1(j,itori,itori1),j=1,6),(v2(j,itori,itori1),j=1,6) + & (v1(j,itori,itori1,1),j=1,6),(v2(j,itori,itori1,1),j=1,6) gloc(i-3,icg)=gloc(i-3,icg)+wtor*fact*gloci c write (iout,*) 'i=',i,' gloc=',gloc(i-3,icg) 1215 continue @@@ -4535,20 -4497,12 +4538,20 @@@ c lprn=.true phii1=phi(i+1) gloci1=0.0D0 gloci2=0.0D0 + iblock=1 + if (iabs(itype(i+1)).eq.20) iblock=2 C Regular cosine and sine terms - do j=1,ntermd_1(itori,itori1,itori2) - v1cij=v1c(1,j,itori,itori1,itori2) - v1sij=v1s(1,j,itori,itori1,itori2) - v2cij=v1c(2,j,itori,itori1,itori2) - v2sij=v1s(2,j,itori,itori1,itori2) +c c do j=1,ntermd_1(itori,itori1,itori2,iblock) +c v1cij=v1c(1,j,itori,itori1,itori2,iblock) +c v1sij=v1s(1,j,itori,itori1,itori2,iblock) +c v2cij=v1c(2,j,itori,itori1,itori2,iblock) +c v2sij=v1s(2,j,itori,itori1,itori2,iblock) + do j=1,ntermd_1(itori,itori1,itori2,iblock) + v1cij=v1c(1,j,itori,itori1,itori2,iblock) + v1sij=v1s(1,j,itori,itori1,itori2,iblock) + v2cij=v1c(2,j,itori,itori1,itori2,iblock) + v2sij=v1s(2,j,itori,itori1,itori2,iblock) + cosphi1=dcos(j*phii) sinphi1=dsin(j*phii) cosphi2=dcos(j*phii1) @@@ -4558,12 -4512,12 +4561,12 @@@ gloci1=gloci1+j*(v1sij*cosphi1-v1cij*sinphi1) gloci2=gloci2+j*(v2sij*cosphi2-v2cij*sinphi2) enddo - do k=2,ntermd_2(itori,itori1,itori2) + do k=2,ntermd_2(itori,itori1,itori2,iblock) do l=1,k-1 - v1cdij = v2c(k,l,itori,itori1,itori2) - v2cdij = v2c(l,k,itori,itori1,itori2) - v1sdij = v2s(k,l,itori,itori1,itori2) - v2sdij = v2s(l,k,itori,itori1,itori2) + v1cdij = v2c(k,l,itori,itori1,itori2,iblock) + v2cdij = v2c(l,k,itori,itori1,itori2,iblock) + v1sdij = v2s(k,l,itori,itori1,itori2,iblock) + v2sdij = v2s(l,k,itori,itori1,itori2,iblock) cosphi1p2=dcos(l*phii+(k-l)*phii1) cosphi1m2=dcos(l*phii-(k-l)*phii1) sinphi1p2=dsin(l*phii+(k-l)*phii1) @@@ -4614,8 -4568,8 +4617,8 @@@ c write (iout,*) "EBACK_SC_COR",it esccor=0.0D0 do i=itau_start,itau_end esccor_ii=0.0D0 - isccori=isccortyp(itype(i-2)) - isccori1=isccortyp(itype(i-1)) + isccori=isccortyp((itype(i-2))) + isccori1=isccortyp((itype(i-1))) phii=phi(i) cccc Added 9 May 2012 cc Tauangle is torsional engle depending on the value of first digit @@@ -4632,14 -4586,14 +4635,14 @@@ c 2 = Ca...Ca...Ca...S c 3 = SC...Ca...Ca...SCi gloci=0.0D0 if (((intertyp.eq.3).and.((itype(i-2).eq.10).or. - & (itype(i-1).eq.10).or.(itype(i-2).eq.21).or. - & (itype(i-1).eq.21))) + & (itype(i-1).eq.10).or.(itype(i-2).eq.ntyp1).or. + & (itype(i-1).eq.ntyp1))) & .or. ((intertyp.eq.1).and.((itype(i-2).eq.10) - & .or.(itype(i-2).eq.21))) + & .or.(itype(i-2).eq.ntyp1))) & .or.((intertyp.eq.2).and.((itype(i-1).eq.10).or. - & (itype(i-1).eq.21)))) cycle - if ((intertyp.eq.2).and.(i.eq.4).and.(itype(1).eq.21)) cycle - if ((intertyp.eq.1).and.(i.eq.nres).and.(itype(nres).eq.21)) + & (itype(i-1).eq.ntyp1)))) cycle + if ((intertyp.eq.2).and.(i.eq.4).and.(itype(1).eq.ntyp1)) cycle + if ((intertyp.eq.1).and.(i.eq.nres).and.(itype(nres).eq.ntyp1)) & cycle do j=1,nterm_sccor(isccori,isccori1) v1ij=v1sccor(j,intertyp,isccori,isccori1) @@@ -4657,7 -4611,7 +4660,7 @@@ c &gloc_sc(intertyp,i-3,icg & restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,itori,itori1, & (v1sccor(j,intertyp,itori,itori1),j=1,6) & ,(v2sccor(j,intertyp,itori,itori1),j=1,6) - gsccor_loc(i-3)=gsccor_loc(i-3)+gloci +c gsccor_loc(i-3)=gsccor_loc(i-3)+gloci enddo !intertyp enddo c do i=1,nres @@@ -4770,9 -4724,9 +4773,9 @@@ c-------------------------------------- integer dimen1,dimen2,atom,indx double precision buffer(dimen1,dimen2) double precision zapas - common /contacts_hb/ zapas(3,20,maxres,7), - & facont_hb(20,maxres),ees0p(20,maxres),ees0m(20,maxres), - & num_cont_hb(maxres),jcont_hb(20,maxres) + common /contacts_hb/ zapas(3,ntyp,maxres,7), + & facont_hb(ntyp,maxres),ees0p(ntyp,maxres),ees0m(ntyp,maxres), + & num_cont_hb(maxres),jcont_hb(ntyp,maxres) num_kont=num_cont_hb(atom) do i=1,num_kont do k=1,7 @@@ -4795,10 -4749,9 +4798,10 @@@ c-------------------------------------- integer dimen1,dimen2,atom,indx double precision buffer(dimen1,dimen2) double precision zapas - common /contacts_hb/ zapas(3,20,maxres,7), - & facont_hb(20,maxres),ees0p(20,maxres),ees0m(20,maxres), - & num_cont_hb(maxres),jcont_hb(20,maxres) + common /contacts_hb/ zapas(3,ntyp,maxres,7), + & facont_hb(ntyp,maxres),ees0p(ntyp,maxres), + & ees0m(ntyp,maxres), + & num_cont_hb(maxres),jcont_hb(ntyp,maxres) num_kont=buffer(1,indx+26) num_kont_old=num_cont_hb(atom) num_cont_hb(atom)=num_kont+num_kont_old