X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fsrc_MD%2Fenergy_p_new_barrier.F;h=2e0ac3774277e9bc85695386647e1ad71c1fa086;hb=78c6b598700d2c701af6532afb20ebc905a0b8ef;hp=851ad39228d816dd55e058b3235357e0aa363c6f;hpb=4866688f3356059b9a933ec2be6da24e6784fa9f;p=unres.git diff --git a/source/unres/src_MD/energy_p_new_barrier.F b/source/unres/src_MD/energy_p_new_barrier.F index 851ad39..2e0ac37 100644 --- a/source/unres/src_MD/energy_p_new_barrier.F +++ b/source/unres/src_MD/energy_p_new_barrier.F @@ -131,6 +131,11 @@ C C Calculate electrostatic (H-bonding) energy of the main chain. C 107 continue +cmc +cmc Sep-06: egb takes care of dynamic ss bonds too +cmc +c if (dyn_ss) call dyn_set_nss + c print *,"Processor",myrank," computed USCSC" #ifdef TIMING #ifdef MPI @@ -326,6 +331,7 @@ C energia(23)=evdw_m c print *," Processor",myrank," calls SUM_ENERGY" call sum_energy(energia,.true.) + if (dyn_ss) call dyn_set_nss c print *," Processor",myrank," left SUM_ENERGY" #ifdef TIMING #ifdef MPI @@ -423,14 +429,14 @@ cMS$ATTRIBUTES C :: proc_proc #ifdef SPLITELE etot=wsc*evdw+wscp*evdw2+welec*ees+wvdwpp*evdw1 & +wang*ebe+wtor*etors+wscloc*escloc - & +wstrain*ehpb+nss*ebr+wcorr*ecorr+wcorr5*ecorr5 + & +wstrain*ehpb+wcorr*ecorr+wcorr5*ecorr5 & +wcorr6*ecorr6+wturn4*eello_turn4+wturn3*eello_turn3 & +wturn6*eturn6+wel_loc*eel_loc+edihcnstr+wtor_d*etors_d & +wbond*estr+Uconst+wsccor*esccor #else etot=wsc*evdw+wscp*evdw2+welec*(ees+evdw1) & +wang*ebe+wtor*etors+wscloc*escloc - & +wstrain*ehpb+nss*ebr+wcorr*ecorr+wcorr5*ecorr5 + & +wstrain*ehpb+wcorr*ecorr+wcorr5*ecorr5 & +wcorr6*ecorr6+wturn4*eello_turn4+wturn3*eello_turn3 & +wturn6*eturn6+wel_loc*eel_loc+edihcnstr+wtor_d*etors_d & +wbond*estr+Uconst+wsccor*esccor @@ -774,7 +780,6 @@ c enddo do i=1,4*nres glocbuf(i)=gloc(i,icg) enddo -#define DEBUG #ifdef DEBUG write (iout,*) "gloc_sc before reduce" do i=1,nres @@ -783,7 +788,6 @@ c enddo enddo enddo #endif -#undef DEBUG do i=1,nres do j=1,3 gloc_scbuf(j,i)=gloc_sc(j,i,icg) @@ -802,7 +806,6 @@ c enddo call MPI_Reduce(gloc_scbuf(1,1),gloc_sc(1,1,icg),3*nres, & MPI_DOUBLE_PRECISION,MPI_SUM,king,FG_COMM,IERR) time_reduce=time_reduce+MPI_Wtime()-time00 -#define DEBUG #ifdef DEBUG write (iout,*) "gloc_sc after reduce" do i=1,nres @@ -811,7 +814,6 @@ c enddo enddo enddo #endif -#undef DEBUG #ifdef DEBUG write (iout,*) "gloc after reduce" do i=1,4*nres @@ -1056,25 +1058,25 @@ C------------------------------------------------------------------------ & edihcnstr,ebr*nss, & Uconst,etot 10 format (/'Virtual-chain energies:'// - & 'EVDW= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-SC)'/ - & 'EVDW2= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-p)'/ - & 'EES= ',1pE16.6,' WEIGHT=',1pD16.6,' (p-p)'/ - & 'EVDWPP=',1pE16.6,' WEIGHT=',1pD16.6,' (p-p VDW)'/ - & 'ESTR= ',1pE16.6,' WEIGHT=',1pD16.6,' (stretching)'/ - & 'EBE= ',1pE16.6,' WEIGHT=',1pD16.6,' (bending)'/ - & 'ESC= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC local)'/ - & 'ETORS= ',1pE16.6,' WEIGHT=',1pD16.6,' (torsional)'/ - & 'ETORSD=',1pE16.6,' WEIGHT=',1pD16.6,' (double torsional)'/ - & 'EHBP= ',1pE16.6,' WEIGHT=',1pD16.6, + & 'EVDW= ',1pE16.6,' WEIGHT=',1pE16.6,' (SC-SC)'/ + & 'EVDW2= ',1pE16.6,' WEIGHT=',1pE16.6,' (SC-p)'/ + & 'EES= ',1pE16.6,' WEIGHT=',1pE16.6,' (p-p)'/ + & 'EVDWPP=',1pE16.6,' WEIGHT=',1pE16.6,' (p-p VDW)'/ + & 'ESTR= ',1pE16.6,' WEIGHT=',1pE16.6,' (stretching)'/ + & 'EBE= ',1pE16.6,' WEIGHT=',1pE16.6,' (bending)'/ + & 'ESC= ',1pE16.6,' WEIGHT=',1pE16.6,' (SC local)'/ + & 'ETORS= ',1pE16.6,' WEIGHT=',1pE16.6,' (torsional)'/ + & 'ETORSD=',1pE16.6,' WEIGHT=',1pE16.6,' (double torsional)'/ + & 'EHPB= ',1pE16.6,' WEIGHT=',1pE16.6, & ' (SS bridges & dist. cnstr.)'/ - & 'ECORR4=',1pE16.6,' WEIGHT=',1pD16.6,' (multi-body)'/ - & 'ECORR5=',1pE16.6,' WEIGHT=',1pD16.6,' (multi-body)'/ - & 'ECORR6=',1pE16.6,' WEIGHT=',1pD16.6,' (multi-body)'/ - & 'EELLO= ',1pE16.6,' WEIGHT=',1pD16.6,' (electrostatic-local)'/ - & 'ETURN3=',1pE16.6,' WEIGHT=',1pD16.6,' (turns, 3rd order)'/ - & 'ETURN4=',1pE16.6,' WEIGHT=',1pD16.6,' (turns, 4th order)'/ - & 'ETURN6=',1pE16.6,' WEIGHT=',1pD16.6,' (turns, 6th order)'/ - & 'ESCCOR=',1pE16.6,' WEIGHT=',1pD16.6,' (backbone-rotamer corr)'/ + & 'ECORR4=',1pE16.6,' WEIGHT=',1pE16.6,' (multi-body)'/ + & 'ECORR5=',1pE16.6,' WEIGHT=',1pE16.6,' (multi-body)'/ + & 'ECORR6=',1pE16.6,' WEIGHT=',1pE16.6,' (multi-body)'/ + & 'EELLO= ',1pE16.6,' WEIGHT=',1pE16.6,' (electrostatic-local)'/ + & 'ETURN3=',1pE16.6,' WEIGHT=',1pE16.6,' (turns, 3rd order)'/ + & 'ETURN4=',1pE16.6,' WEIGHT=',1pE16.6,' (turns, 4th order)'/ + & 'ETURN6=',1pE16.6,' WEIGHT=',1pE16.6,' (turns, 6th order)'/ + & 'ESCCOR=',1pE16.6,' WEIGHT=',1pE16.6,' (backbone-rotamer corr)'/ & 'EDIHC= ',1pE16.6,' (dihedral angle constraints)'/ & 'ESS= ',1pE16.6,' (disulfide-bridge intrinsic energy)'/ & 'UCONST= ',1pE16.6,' (Constraint energy)'/ @@ -1447,7 +1449,7 @@ C 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) @@ -1556,6 +1558,7 @@ C include 'COMMON.IOUNITS' include 'COMMON.CALC' include 'COMMON.CONTROL' + include 'COMMON.SBRIDGE' logical lprn evdw=0.0D0 ccccc energy_dec=.false. @@ -1584,6 +1587,12 @@ C Calculate SC interaction energy. C do iint=1,nint_gr(i) do j=istart(i,iint),iend(i,iint) + IF (dyn_ss_mask(i).and.dyn_ss_mask(j)) THEN + call dyn_ssbond_ene(i,j,evdwij) + evdw=evdw+evdwij + if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a3)') + & 'evdw',i,j,evdwij,' ss' + ELSE ind=ind+1 itypj=itype(j) c dscj_inv=dsc_inv(itypj) @@ -1693,6 +1702,7 @@ C Calculate angular part of the gradient. #else call sc_grad #endif + ENDIF ! dyn_ss enddo ! j enddo ! iint enddo ! i @@ -4266,49 +4276,96 @@ C iii and jjj point to the residues for which the distance is assigned. iii=ii jjj=jj endif -cd write (iout,*) "i",i," ii",ii," iii",iii," jj",jj," jjj",jjj +c write (iout,*) "i",i," ii",ii," iii",iii," jj",jj," jjj",jjj, +c & dhpb(i),dhpb1(i),forcon(i) C 24/11/03 AL: SS bridges handled separately because of introducing a specific C distance and angle dependent SS bond potential. - if (ii.gt.nres .and. itype(iii).eq.1 .and. itype(jjj).eq.1) then +cmc if (ii.gt.nres .and. itype(iii).eq.1 .and. itype(jjj).eq.1) then +C 18/07/06 MC: Use the convention that the first nss pairs are SS bonds + 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 call ssbond_ene(iii,jjj,eij) ehpb=ehpb+2*eij + endif cd write (iout,*) "eij",eij + else if (ii.gt.nres .and. jj.gt.nres) then +c Restraints from contact prediction + dd=dist(ii,jj) + if (dhpb1(i).gt.0.0d0) then + ehpb=ehpb+2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i)) + fac=forcon(i)*gnmr1prim(dd,dhpb(i),dhpb1(i))/dd +c write (iout,*) "beta nmr", +c & dd,2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i)) + else + dd=dist(ii,jj) + rdis=dd-dhpb(i) +C Get the force constant corresponding to this distance. + waga=forcon(i) +C Calculate the contribution to energy. + ehpb=ehpb+waga*rdis*rdis +c write (iout,*) "beta reg",dd,waga*rdis*rdis +C +C Evaluate gradient. +C + fac=waga*rdis/dd + endif + do j=1,3 + ggg(j)=fac*(c(j,jj)-c(j,ii)) + enddo + do j=1,3 + ghpbx(j,iii)=ghpbx(j,iii)-ggg(j) + ghpbx(j,jjj)=ghpbx(j,jjj)+ggg(j) + enddo + do k=1,3 + ghpbc(k,jjj)=ghpbc(k,jjj)+ggg(k) + ghpbc(k,iii)=ghpbc(k,iii)-ggg(k) + enddo 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) + if (dhpb1(i).gt.0.0d0) then + ehpb=ehpb+2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i)) + fac=forcon(i)*gnmr1prim(dd,dhpb(i),dhpb1(i))/dd +c write (iout,*) "alph nmr", +c & dd,2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i)) + else + 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 write (iout,*) "alpha reg",dd,waga*rdis*rdis C C Evaluate gradient. C - fac=waga*rdis/dd + fac=waga*rdis/dd + endif 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 @@ -4370,7 +4427,7 @@ c dscj_inv=dsc_inv(itypj) deltat12=om2-om1+2.0d0 cosphi=om12-om1*om2 eij=akcm*deltad*deltad+akth*(deltat1*deltat1+deltat2*deltat2) - & +akct*deltad*deltat12 + & +akct*deltad*deltat12+ebr & +v1ss*cosphi+v2ss*cosphi*cosphi+v3ss*cosphi*cosphi*cosphi c write(iout,*) i,j,"rij",rij,"d0cm",d0cm," akcm",akcm," akth",akth, c & " akct",akct," deltad",deltad," deltat",deltat1,deltat2, @@ -4512,6 +4569,18 @@ c write (*,'(a,i2)') 'EBEND ICG=',icg 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) @@ -4545,15 +4614,27 @@ C dependent on the adjacent virtual-bond-valence angles (gamma1 & gamma2). 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) @@ -4751,6 +4832,9 @@ C 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 @@ -4771,7 +4855,7 @@ C 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) @@ -4793,11 +4877,12 @@ C 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 @@ -4816,24 +4901,24 @@ C 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) @@ -4841,28 +4926,33 @@ C 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) @@ -4871,9 +4961,11 @@ C 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 @@ -5214,7 +5306,7 @@ C 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 @@ -5232,7 +5324,7 @@ 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) @@ -5264,7 +5356,7 @@ C 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 @@ -5272,7 +5364,7 @@ c write (2,*) "xx",xx," yy",yy," zz",zz 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 @@ -5442,8 +5534,10 @@ c & (dC_norm(j,i-1),j=1,3)," vbld_inv",vbld_inv(i+1),vbld_inv(i) 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)) @@ -5729,6 +5823,8 @@ c lprn=.true. etors=0.0D0 do i=iphi_start,iphi_end etors_ii=0.0D0 +c if (itype(i-2).eq.ntyp1 .or. itype(i-1).eq.ntyp1 +c & .or. itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle itori=itortyp(itype(i-2)) itori1=itortyp(itype(i-1)) phii=phi(i) @@ -5822,6 +5918,8 @@ C Set lprn=.true. for debugging c lprn=.true. etors_d=0.0D0 do i=iphid_start,iphid_end +c if (itype(i-2).eq.ntyp1 .or. itype(i-1).eq.ntyp1 +c & .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)) @@ -5894,10 +5992,11 @@ 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) @@ -5916,14 +6015,16 @@ c 2 = Ca...Ca...Ca...SC 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) @@ -5938,9 +6039,9 @@ c write (iout,*) "WTF",intertyp,i,itype(i),v1ij*cosphi+v2ij*sinphi 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 @@ -8053,9 +8154,9 @@ C C Parallel Antiparallel C C o o -C /l\ /j\ -C / \ / \ -C /| o | | o |\ +C /l\ /j\ +C / \ / \ +C /| o | | o |\ C \ j|/k\| / \ |/k\|l / C \ / \ / \ / \ / C o o o o @@ -8150,22 +8251,22 @@ c---------------------------------------------------------------------------- include 'COMMON.GEO' logical swap double precision vv(2),pizda(2,2),auxmat(2,2),auxvec(2), - & auxvec1(2),auxvec2(1),auxmat1(2,2) + & auxvec1(2),auxvec2(2),auxmat1(2,2) logical lprn common /kutas/ lprn CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC -C -C Parallel Antiparallel -C -C o o -C \ /l\ /j\ / -C \ / \ / \ / -C o| o | | o |o -C \ j|/k\| \ |/k\|l -C \ / \ \ / \ -C o o -C i i -C +C C +C Parallel Antiparallel C +C C +C o o C +C \ /l\ /j\ / C +C \ / \ / \ / 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 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, @@ -8336,18 +8437,18 @@ c---------------------------------------------------------------------------- double precision vv(2),pizda(2,2),auxmat(2,2),auxvec(2) logical swap CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC -C -C Parallel Antiparallel -C -C o o -C /l\ / \ /j\ -C / \ / \ / \ -C /| o |o o| o |\ -C j|/k\| / |/k\|l / -C / \ / / \ / -C / o / o -C i i -C +C C +C Parallel Antiparallel C +C C +C o o C +C /l\ / \ /j\ C +C / \ / \ / \ 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 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC C C 4/7/01 AL Component s1 was removed, because it pertains to the respective @@ -8453,18 +8554,18 @@ c---------------------------------------------------------------------------- & auxvec1(2),auxmat1(2,2) logical swap CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC -C -C Parallel Antiparallel -C -C o o -C /l\ / \ /j\ -C / \ / \ / \ -C /| o |o o| o |\ -C \ j|/k\| \ |/k\|l -C \ / \ \ / \ -C o \ o \ -C i i -C +C C +C Parallel Antiparallel C +C C +C o o C +C /l\ / \ /j\ C +C / \ / \ / \ 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 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC C C 4/7/01 AL Component s1 was removed, because it pertains to the respective