X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Fcluster%2Fwham%2Fsrc-M%2Fenergy_p_new.F;h=66d6a2668a293fc606cc8b32e6c6eac34a50eb12;hb=15cbe2fc81082e6828fa504b3b22499600134b54;hp=aa1ef75fea80b1adaa3cc888e939cf009a065e57;hpb=478a9d9a1c99eb3f4bc4ca676ff3162bdd01d633;p=unres.git diff --git a/source/cluster/wham/src-M/energy_p_new.F b/source/cluster/wham/src-M/energy_p_new.F index aa1ef75..66d6a26 100644 --- a/source/cluster/wham/src-M/energy_p_new.F +++ b/source/cluster/wham/src-M/energy_p_new.F @@ -1,7 +1,6 @@ subroutine etotal(energia,fact) implicit real*8 (a-h,o-z) include 'DIMENSIONS' - include 'sizesclu.dat' #ifndef ISNAN external proc_proc @@ -12,18 +11,17 @@ cMS$ATTRIBUTES C :: proc_proc include 'COMMON.IOUNITS' double precision energia(0:max_ene),energia1(0:max_ene+1) -#ifdef MPL - include 'COMMON.INFO' - external d_vadd - integer ready -#endif include 'COMMON.FFIELD' include 'COMMON.DERIV' include 'COMMON.INTERACT' include 'COMMON.SBRIDGE' include 'COMMON.CHAIN' + include 'COMMON.SHIELD' + include 'COMMON.CONTROL' + include 'COMMON.TORCNSTR' double precision fact(6) -cd write(iout, '(a,i2)')'Calling etotal ipot=',ipot +c write(iout, '(a,i2)')'Calling etotal ipot=',ipot +c call flush(iout) cd print *,'nnt=',nnt,' nct=',nct C C Compute the side-chain and electrostatic interaction energy @@ -47,8 +45,19 @@ C Gay-Berne-Vorobjev potential (shifted LJ, angular dependence). C C Calculate electrostatic (H-bonding) energy of the main chain. C - 106 call eelec(ees,evdw1,eel_loc,eello_turn3,eello_turn4) -C + 106 continue +c write (iout,*) "Sidechain" + call flush(iout) + call vec_and_deriv + if (shield_mode.eq.1) then + call set_shield_fac + else if (shield_mode.eq.2) then + call set_shield_fac2 + endif + call eelec(ees,evdw1,eel_loc,eello_turn3,eello_turn4) +c write(iout,*) 'po eelec' +c call flush(iout) + C Calculate excluded-volume interaction energy between peptide groups C and side chains. C @@ -56,8 +65,9 @@ C c c Calculate the bond-stretching energy c + call ebond(estr) -c write (iout,*) "estr",estr +C write (iout,*) "estr",estr C C Calculate the disulfide-bridge and other energy and the contributions C from other distance constraints. @@ -67,26 +77,60 @@ cd print *,'EHPB exitted succesfully.' C C Calculate the virtual-bond-angle energy. C - call ebend(ebe) +C print *,'Bend energy finished.' + if (wang.gt.0d0) then + if (tor_mode.eq.0) then + call ebend(ebe) + else +C ebend kcc is Kubo cumulant clustered rigorous attemp to derive the +C energy function + call ebend_kcc(ebe) + endif + else + ebe=0.0d0 + endif + ethetacnstr=0.0d0 + if (with_theta_constr) call etheta_constr(ethetacnstr) +c call ebend(ebe,ethetacnstr) cd print *,'Bend energy finished.' C C Calculate the SC local energy. C call esc(escloc) -cd print *,'SCLOC energy finished.' +C print *,'SCLOC energy finished.' C C Calculate the virtual-bond torsional energy. C -cd print *,'nterm=',nterm - call etor(etors,edihcnstr,fact(1)) + if (wtor.gt.0.0d0) then + if (tor_mode.eq.0) then + call etor(etors,fact(1)) + else +C etor kcc is Kubo cumulant clustered rigorous attemp to derive the +C energy function + call etor_kcc(etors,fact(1)) + endif + else + etors=0.0d0 + endif + edihcnstr=0.0d0 + if (ndih_constr.gt.0) call etor_constr(edihcnstr) +c print *,"Processor",myrank," computed Utor" C C 6/23/01 Calculate double-torsional energy C - call etor_d(etors_d,fact(2)) -C -C 21/5/07 Calculate local sicdechain correlation energy + if ((wtor_d.gt.0.0d0).and.(tor_mode.eq.0)) then + call etor_d(etors_d,fact(2)) + else + etors_d=0 + endif +c print *,"Processor",myrank," computed Utord" C call eback_sc_corr(esccor) + + if (wliptran.gt.0) then + call Eliptransfer(eliptran) + endif + C C 12/1/95 Multi-body terms C @@ -94,37 +138,69 @@ C n_corr1=0 if (wcorr4.gt.0.0d0 .or. wcorr5.gt.0.0d0 .or. wcorr6.gt.0.0d0 & .or. wturn6.gt.0.0d0) then -c print *,"calling multibody_eello" +c write(iout,*)"calling multibody_eello" call multibody_eello(ecorr,ecorr5,ecorr6,eturn6,n_corr,n_corr1) -c write (*,*) 'n_corr=',n_corr,' n_corr1=',n_corr1 -c print *,ecorr,ecorr5,ecorr6,eturn6 +c write (iout,*) 'n_corr=',n_corr,' n_corr1=',n_corr1 +c write (iout,*) ecorr,ecorr5,ecorr6,eturn6 + else + ecorr=0.0d0 + ecorr5=0.0d0 + ecorr6=0.0d0 + eturn6=0.0d0 endif if (wcorr4.eq.0.0d0 .and. wcorr.gt.0.0d0) then +c write (iout,*) "Calling multibody_hbond" call multibody_hb(ecorr,ecorr5,ecorr6,n_corr,n_corr1) endif c write (iout,*) "ft(6)",fact(6)," evdw",evdw," evdw_t",evdw_t #ifdef SPLITELE + if (shield_mode.gt.0) then + etot=fact(1)*wsc*(evdw+fact(6)*evdw_t)+fact(1)*wscp*evdw2 + & +welec*fact(1)*ees + & +fact(1)*wvdwpp*evdw1 + & +wang*ebe+wtor*fact(1)*etors+wscloc*escloc + & +wstrain*ehpb+wcorr*fact(3)*ecorr+wcorr5*fact(4)*ecorr5 + & +wcorr6*fact(5)*ecorr6+wturn4*fact(3)*eello_turn4 + & +wturn3*fact(2)*eello_turn3+wturn6*fact(5)*eturn6 + & +wel_loc*fact(2)*eel_loc+edihcnstr+wtor_d*fact(2)*etors_d + & +wbond*estr+wsccor*fact(1)*esccor+ethetacnstr + & +wliptran*eliptran + else etot=wsc*(evdw+fact(6)*evdw_t)+wscp*evdw2+welec*fact(1)*ees & +wvdwpp*evdw1 & +wang*ebe+wtor*fact(1)*etors+wscloc*escloc - & +wstrain*ehpb+nss*ebr+wcorr*fact(3)*ecorr+wcorr5*fact(4)*ecorr5 + & +wstrain*ehpb+wcorr*fact(3)*ecorr+wcorr5*fact(4)*ecorr5 & +wcorr6*fact(5)*ecorr6+wturn4*fact(3)*eello_turn4 & +wturn3*fact(2)*eello_turn3+wturn6*fact(5)*eturn6 & +wel_loc*fact(2)*eel_loc+edihcnstr+wtor_d*fact(2)*etors_d - & +wbond*estr+wsccor*fact(1)*esccor + & +wbond*estr+wsccor*fact(1)*esccor+ethetacnstr + & +wliptran*eliptran + endif #else + if (shield_mode.gt.0) then + etot=fact(1)wsc*(evdw+fact(6)*evdw_t)+fact(1)*wscp*evdw2 + & +welec*fact(1)*(ees+evdw1) + & +wang*ebe+wtor*fact(1)*etors+wscloc*escloc + & +wstrain*ehpb+wcorr*fact(3)*ecorr+wcorr5*fact(4)*ecorr5 + & +wcorr6*fact(5)*ecorr6+wturn4*fact(3)*eello_turn4 + & +wturn3*fact(2)*eello_turn3+wturn6*fact(5)*eturn6 + & +wel_loc*fact(2)*eel_loc+edihcnstr+wtor_d*fact(2)*etors_d + & +wbond*estr+wsccor*fact(1)*esccor+ethetacnstr + & +wliptran*eliptran + else etot=wsc*(evdw+fact(6)*evdw_t)+wscp*evdw2 & +welec*fact(1)*(ees+evdw1) & +wang*ebe+wtor*fact(1)*etors+wscloc*escloc - & +wstrain*ehpb+nss*ebr+wcorr*fact(3)*ecorr+wcorr5*fact(4)*ecorr5 + & +wstrain*ehpb+wcorr*fact(3)*ecorr+wcorr5*fact(4)*ecorr5 & +wcorr6*fact(5)*ecorr6+wturn4*fact(3)*eello_turn4 & +wturn3*fact(2)*eello_turn3+wturn6*fact(5)*eturn6 & +wel_loc*fact(2)*eel_loc+edihcnstr+wtor_d*fact(2)*etors_d - & +wbond*estr+wsccor*fact(1)*esccor + & +wbond*estr+wsccor*fact(1)*esccor+ethetacnstr + & +wliptran*eliptran + endif #endif energia(0)=etot energia(1)=evdw -c call enerprint(energia(0),frac) #ifdef SCP14 energia(2)=evdw2-evdw2_14 energia(17)=evdw2_14 @@ -155,6 +231,8 @@ c call enerprint(energia(0),frac) energia(19)=esccor energia(20)=edihcnstr energia(21)=evdw_t + energia(24)=ethetacnstr + energia(22)=eliptran c detecting NaNQ #ifdef ISNAN #ifdef AIX @@ -174,6 +252,9 @@ c detecting NaNQ #ifdef MPL c endif #endif +#ifdef DEBUG + call enerprint(energia,fact) +#endif if (calc_grad) then C C Sum up the components of the Cartesian gradient. @@ -181,6 +262,7 @@ C #ifdef SPLITELE do i=1,nct do j=1,3 + if (shield_mode.eq.0) then gradc(j,i,icg)=wsc*gvdwc(j,i)+wscp*gvdwc_scp(j,i)+ & welec*fact(1)*gelc(j,i)+wvdwpp*gvdwpp(j,i)+ & wbond*gradb(j,i)+ @@ -193,14 +275,57 @@ C & wcorr6*fact(5)*gradcorr6(j,i)+ & wturn6*fact(5)*gcorr6_turn(j,i)+ & wsccor*fact(2)*gsccorc(j,i) + & +wliptran*gliptranc(j,i) gradx(j,i,icg)=wsc*gvdwx(j,i)+wscp*gradx_scp(j,i)+ & wbond*gradbx(j,i)+ & wstrain*ghpbx(j,i)+wcorr*gradxorr(j,i)+ & wsccor*fact(2)*gsccorx(j,i) + & +wliptran*gliptranx(j,i) + else + gradc(j,i,icg)=fact(1)*wsc*gvdwc(j,i) + & +fact(1)*wscp*gvdwc_scp(j,i)+ + & welec*fact(1)*gelc(j,i)+fact(1)*wvdwpp*gvdwpp(j,i)+ + & wbond*gradb(j,i)+ + & wstrain*ghpbc(j,i)+ + & wcorr*fact(3)*gradcorr(j,i)+ + & wel_loc*fact(2)*gel_loc(j,i)+ + & wturn3*fact(2)*gcorr3_turn(j,i)+ + & wturn4*fact(3)*gcorr4_turn(j,i)+ + & wcorr5*fact(4)*gradcorr5(j,i)+ + & wcorr6*fact(5)*gradcorr6(j,i)+ + & wturn6*fact(5)*gcorr6_turn(j,i)+ + & wsccor*fact(2)*gsccorc(j,i) + & +wliptran*gliptranc(j,i) + & +welec*gshieldc(j,i) + & +welec*gshieldc_loc(j,i) + & +wcorr*gshieldc_ec(j,i) + & +wcorr*gshieldc_loc_ec(j,i) + & +wturn3*gshieldc_t3(j,i) + & +wturn3*gshieldc_loc_t3(j,i) + & +wturn4*gshieldc_t4(j,i) + & +wturn4*gshieldc_loc_t4(j,i) + & +wel_loc*gshieldc_ll(j,i) + & +wel_loc*gshieldc_loc_ll(j,i) + + gradx(j,i,icg)=fact(1)*wsc*gvdwx(j,i) + & +fact(1)*wscp*gradx_scp(j,i)+ + & wbond*gradbx(j,i)+ + & wstrain*ghpbx(j,i)+wcorr*gradxorr(j,i)+ + & wsccor*fact(2)*gsccorx(j,i) + & +wliptran*gliptranx(j,i) + & +welec*gshieldx(j,i) + & +wcorr*gshieldx_ec(j,i) + & +wturn3*gshieldx_t3(j,i) + & +wturn4*gshieldx_t4(j,i) + & +wel_loc*gshieldx_ll(j,i) + + + endif enddo #else do i=1,nct do j=1,3 + if (shield_mode.eq.0) then gradc(j,i,icg)=wsc*gvdwc(j,i)+wscp*gvdwc_scp(j,i)+ & welec*fact(1)*gelc(j,i)+wstrain*ghpbc(j,i)+ & wbond*gradb(j,i)+ @@ -212,10 +337,50 @@ C & wcorr6*fact(5)*gradcorr6(j,i)+ & wturn6*fact(5)*gcorr6_turn(j,i)+ & wsccor*fact(2)*gsccorc(j,i) + & +wliptran*gliptranc(j,i) gradx(j,i,icg)=wsc*gvdwx(j,i)+wscp*gradx_scp(j,i)+ & wbond*gradbx(j,i)+ & wstrain*ghpbx(j,i)+wcorr*gradxorr(j,i)+ & wsccor*fact(1)*gsccorx(j,i) + & +wliptran*gliptranx(j,i) + else + gradc(j,i,icg)=fact(1)*wsc*gvdwc(j,i)+ + & fact(1)*wscp*gvdwc_scp(j,i)+ + & welec*fact(1)*gelc(j,i)+wstrain*ghpbc(j,i)+ + & wbond*gradb(j,i)+ + & wcorr*fact(3)*gradcorr(j,i)+ + & wel_loc*fact(2)*gel_loc(j,i)+ + & wturn3*fact(2)*gcorr3_turn(j,i)+ + & wturn4*fact(3)*gcorr4_turn(j,i)+ + & wcorr5*fact(4)*gradcorr5(j,i)+ + & wcorr6*fact(5)*gradcorr6(j,i)+ + & wturn6*fact(5)*gcorr6_turn(j,i)+ + & wsccor*fact(2)*gsccorc(j,i) + & +wliptran*gliptranc(j,i) + & +welec*gshieldc(j,i) + & +welec*gshieldc_loc(j,i) + & +wcorr*gshieldc_ec(j,i) + & +wcorr*gshieldc_loc_ec(j,i) + & +wturn3*gshieldc_t3(j,i) + & +wturn3*gshieldc_loc_t3(j,i) + & +wturn4*gshieldc_t4(j,i) + & +wturn4*gshieldc_loc_t4(j,i) + & +wel_loc*gshieldc_ll(j,i) + & +wel_loc*gshieldc_loc_ll(j,i) + + gradx(j,i,icg)=fact(1)*wsc*gvdwx(j,i)+ + & fact(1)*wscp*gradx_scp(j,i)+ + & wbond*gradbx(j,i)+ + & wstrain*ghpbx(j,i)+wcorr*gradxorr(j,i)+ + & wsccor*fact(1)*gsccorx(j,i) + & +wliptran*gliptranx(j,i) + & +welec*gshieldx(j,i) + & +wcorr*gshieldx_ec(j,i) + & +wturn3*gshieldx_t3(j,i) + & +wturn4*gshieldx_t4(j,i) + & +wel_loc*gshieldx_ll(j,i) + + endif enddo #endif enddo @@ -229,16 +394,17 @@ C & +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) +c BYLA ROZNICA Z CLUSTER< OSTATNIA LINIA DODANA enddo endif + if (dyn_ss) call dyn_set_nss return end C------------------------------------------------------------------------ subroutine enerprint(energia,fact) implicit real*8 (a-h,o-z) include 'DIMENSIONS' - include 'sizesclu.dat' include 'COMMON.IOUNITS' include 'COMMON.FFIELD' include 'COMMON.SBRIDGE' @@ -269,6 +435,8 @@ C------------------------------------------------------------------------ esccor=energia(19) edihcnstr=energia(20) estr=energia(18) + ethetacnstr=energia(24) + eliptran=energia(22) #ifdef SPLITELE write (iout,10) evdw,wsc,evdw2,wscp,ees,welec*fact(1),evdw1, & wvdwpp, @@ -277,7 +445,8 @@ C------------------------------------------------------------------------ & ecorr,wcorr*fact(3),ecorr5,wcorr5*fact(4),ecorr6,wcorr6*fact(5), & eel_loc,wel_loc*fact(2),eello_turn3,wturn3*fact(2), & eello_turn4,wturn4*fact(3),eello_turn6,wturn6*fact(5), - & esccor,wsccor*fact(1),edihcnstr,ebr*nss,etot + & esccor,wsccor*fact(1),edihcnstr,ethetacnstr,ebr*nss, + & eliptran,wliptran,etot 10 format (/'Virtual-chain energies:'// & 'EVDW= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-SC)'/ & 'EVDW2= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-p)'/ @@ -299,7 +468,9 @@ C------------------------------------------------------------------------ & 'ETURN6=',1pE16.6,' WEIGHT=',1pD16.6,' (turns, 6th order)'/ & 'ESCCOR=',1pE16.6,' WEIGHT=',1pD16.6,' (backbone-rotamer corr)'/ & 'EDIHC= ',1pE16.6,' (dihedral angle constraints)'/ + & 'ETHETC= ',1pE16.6,' (valence angle constraints)'/ & 'ESS= ',1pE16.6,' (disulfide-bridge intrinsic energy)'/ + & 'ELT=',1pE16.6, ' WEIGHT=',1pD16.6,' (Lipid transfer energy)'/ & 'ETOT= ',1pE16.6,' (total)') #else write (iout,10) evdw,wsc,evdw2,wscp,ees,welec*fact(1),estr,wbond, @@ -308,7 +479,7 @@ C------------------------------------------------------------------------ & ecorr6,wcorr6*fact(5),eel_loc,wel_loc*fact(2), & eello_turn3,wturn3*fact(2),eello_turn4,wturn4*fact(3), & eello_turn6,wturn6*fact(5),esccor*fact(1),wsccor, - & edihcnstr,ebr*nss,etot + & edihcnstr,ethetacnstr,ebr*nss,eliptran,wliptran,etot 10 format (/'Virtual-chain energies:'// & 'EVDW= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-SC)'/ & 'EVDW2= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-p)'/ @@ -329,7 +500,9 @@ C------------------------------------------------------------------------ & 'ETURN6=',1pE16.6,' WEIGHT=',1pD16.6,' (turns, 6th order)'/ & 'ESCCOR=',1pE16.6,' WEIGHT=',1pD16.6,' (backbone-rotamer corr)'/ & 'EDIHC= ',1pE16.6,' (dihedral angle constraints)'/ + & 'ETHETC= ',1pE16.6,' (valence angle constraints)'/ & 'ESS= ',1pE16.6,' (disulfide-bridge intrinsic energy)'/ + & 'ELT=',1pE16.6, ' WEIGHT=',1pD16.6,' (Lipid transfer energy)'/ & 'ETOT= ',1pE16.6,' (total)') #endif return @@ -342,7 +515,6 @@ C assuming the LJ potential of interaction. C implicit real*8 (a-h,o-z) include 'DIMENSIONS' - include 'sizesclu.dat' include "DIMENSIONS.COMPAR" parameter (accur=1.0d-10) include 'COMMON.GEO' @@ -360,12 +532,20 @@ C integer icant external icant cd print *,'Entering ELJ nnt=',nnt,' nct=',nct,' expon=',expon +c ROZNICA z cluster +c do i=1,210 +c do j=1,2 +c eneps_temp(j,i)=0.0d0 +c enddo +c enddo +cROZNICA + evdw=0.0D0 evdw_t=0.0d0 do i=iatsc_s,iatsc_e - itypi=itype(i) - if (itypi.eq.21) cycle - 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) @@ -378,8 +558,8 @@ C 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) - if (itypj.eq.21) cycle + 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 @@ -389,17 +569,22 @@ C Change 12/1/95 to calculate four-body interactions c write (iout,*)'i=',i,' j=',j,' itypi=',itypi,' itypj=',itypj eps0ij=eps(itypi,itypj) fac=rrij**expon2 - e1=fac*fac*aa(itypi,itypj) - e2=fac*bb(itypi,itypj) + e1=fac*fac*aa + e2=fac*bb evdwij=e1+e2 ij=icant(itypi,itypj) +c ROZNICA z cluster +c eneps_temp(1,ij)=eneps_temp(1,ij)+e1/dabs(eps0ij) +c eneps_temp(2,ij)=eneps_temp(2,ij)+e2/eps0ij +c + cd sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0) cd epsi=bb(itypi,itypj)**2/aa(itypi,itypj) cd write (iout,'(2(a3,i3,2x),6(1pd12.4)/2(3(1pd12.4),5x)/)') cd & restyp(itypi),i,restyp(itypj),j,aa(itypi,itypj), cd & bb(itypi,itypj),1.0D0/dsqrt(rrij),evdwij,epsi,sigm, cd & (c(k,i),k=1,3),(c(k,j),k=1,3) - if (bb(itypi,itypj).gt.0.0d0) then + if (bb.gt.0.0d0) then evdw=evdw+evdwij else evdw_t=evdw_t+evdwij @@ -510,7 +695,6 @@ C assuming the LJK potential of interaction. C implicit real*8 (a-h,o-z) include 'DIMENSIONS' - include 'sizesclu.dat' include "DIMENSIONS.COMPAR" include 'COMMON.GEO' include 'COMMON.VAR' @@ -525,12 +709,17 @@ C integer icant external icant c print *,'Entering ELJK nnt=',nnt,' nct=',nct,' expon=',expon +c do i=1,210 +c do j=1,2 +c eneps_temp(j,i)=0.0d0 +c enddo +c enddo evdw=0.0D0 evdw_t=0.0d0 do i=iatsc_s,iatsc_e - itypi=itype(i) - if (itypi.eq.21) cycle - 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) @@ -539,8 +728,8 @@ C Calculate SC interaction energy. C do iint=1,nint_gr(i) do j=istart(i,iint),iend(i,iint) - itypj=itype(j) - if (itypj.eq.21) cycle + 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 @@ -551,10 +740,13 @@ C rij=1.0D0/r_inv_ij r_shift_inv=1.0D0/(rij+r0(itypi,itypj)-sigma(itypi,itypj)) fac=r_shift_inv**expon - e1=fac*fac*aa(itypi,itypj) - e2=fac*bb(itypi,itypj) + e1=fac*fac*aa + e2=fac*bb evdwij=e_augm+e1+e2 ij=icant(itypi,itypj) +c eneps_temp(1,ij)=eneps_temp(1,ij)+(e1+a_augm) +c & /dabs(eps(itypi,itypj)) +c eneps_temp(2,ij)=eneps_temp(2,ij)+e2/eps(itypi,itypj) cd sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0) cd epsi=bb(itypi,itypj)**2/aa(itypi,itypj) cd write (iout,'(2(a3,i3,2x),8(1pd12.4)/2(3(1pd12.4),5x)/)') @@ -562,7 +754,7 @@ cd & restyp(itypi),i,restyp(itypj),j,aa(itypi,itypj), cd & bb(itypi,itypj),augm(itypi,itypj),epsi,sigm, cd & sigma(itypi,itypj),1.0D0/dsqrt(rrij),evdwij, cd & (c(k,i),k=1,3),(c(k,j),k=1,3) - if (bb(itypi,itypj).gt.0.0d0) then + if (bb.gt.0.0d0) then evdw=evdw+evdwij else evdw_t=evdw_t+evdwij @@ -606,7 +798,6 @@ C assuming the Berne-Pechukas potential of interaction. C implicit real*8 (a-h,o-z) include 'DIMENSIONS' - include 'sizesclu.dat' include "DIMENSIONS.COMPAR" include 'COMMON.GEO' include 'COMMON.VAR' @@ -622,6 +813,11 @@ c double precision rrsave(maxdim) logical lprn integer icant external icant +c do i=1,210 +c do j=1,2 +c eneps_temp(j,i)=0.0d0 +c enddo +c enddo evdw=0.0D0 evdw_t=0.0d0 c print *,'Entering EBP nnt=',nnt,' nct=',nct,' expon=',expon @@ -632,9 +828,9 @@ c else c endif ind=0 do i=iatsc_s,iatsc_e - itypi=itype(i) - if (itypi.eq.21) cycle - 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) @@ -648,8 +844,8 @@ C do iint=1,nint_gr(i) do j=istart(i,iint),iend(i,iint) ind=ind+1 - itypj=itype(j) - if (itypj.eq.21) cycle + itypj=iabs(itype(j)) + if (itypj.eq.ntyp1) cycle dscj_inv=vbld_inv(j+nres) chi1=chi(itypi,itypj) chi2=chi(itypj,itypi) @@ -688,29 +884,32 @@ C Calculate the angle-dependent terms of energy & contributions to derivatives. C Calculate whole angle-dependent part of epsilon and contributions C to its derivatives fac=(rrij*sigsq)**expon2 - e1=fac*fac*aa(itypi,itypj) - e2=fac*bb(itypi,itypj) + e1=fac*fac*aa + e2=fac*bb evdwij=eps1*eps2rt*eps3rt*(e1+e2) eps2der=evdwij*eps3rt eps3der=evdwij*eps2rt evdwij=evdwij*eps2rt*eps3rt ij=icant(itypi,itypj) aux=eps1*eps2rt**2*eps3rt**2 - if (bb(itypi,itypj).gt.0.0d0) then +c eneps_temp(1,ij)=eneps_temp(1,ij)+e1*aux +c & /dabs(eps(itypi,itypj)) +c eneps_temp(2,ij)=eneps_temp(2,ij)+e2*aux/eps(itypi,itypj) + if (bb.gt.0.0d0) then evdw=evdw+evdwij else evdw_t=evdw_t+evdwij endif if (calc_grad) then if (lprn) then - sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0) - epsi=bb(itypi,itypj)**2/aa(itypi,itypj) -cd write (iout,'(2(a3,i3,2x),15(0pf7.3))') -cd & restyp(itypi),i,restyp(itypj),j, -cd & epsi,sigm,chi1,chi2,chip1,chip2, -cd & eps1,eps2rt**2,eps3rt**2,1.0D0/dsqrt(sigsq), -cd & om1,om2,om12,1.0D0/dsqrt(rrij), -cd & evdwij + sigm=dabs(aa/bb)**(1.0D0/6.0D0) + epsi=bb**2/aa + write (iout,'(2(a3,i3,2x),15(0pf7.3))') + & restyp(itypi),i,restyp(itypj),j, + & epsi,sigm,chi1,chi2,chip1,chip2, + & eps1,eps2rt**2,eps3rt**2,1.0D0/dsqrt(sigsq), + & om1,om2,om12,1.0D0/dsqrt(rrij), + & evdwij endif C Calculate gradient components. e1=e1*eps1*eps2rt**2*eps3rt**2 @@ -739,7 +938,6 @@ C assuming the Gay-Berne potential of interaction. C implicit real*8 (a-h,o-z) include 'DIMENSIONS' - include 'sizesclu.dat' include "DIMENSIONS.COMPAR" include 'COMMON.GEO' include 'COMMON.VAR' @@ -750,10 +948,16 @@ C include 'COMMON.INTERACT' include 'COMMON.IOUNITS' include 'COMMON.CALC' + include 'COMMON.SBRIDGE' logical lprn common /srutu/icall - integer icant + integer icant,xshift,yshift,zshift external icant +c do i=1,210 +c do j=1,2 +c eneps_temp(j,i)=0.0d0 +c enddo +c enddo c print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon evdw=0.0D0 evdw_t=0.0d0 @@ -761,12 +965,42 @@ c print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon c if (icall.gt.0) lprn=.true. ind=0 do i=iatsc_s,iatsc_e - itypi=itype(i) - if (itypi.eq.21) cycle - 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) +C returning the ith atom to box + xi=mod(xi,boxxsize) + if (xi.lt.0) xi=xi+boxxsize + yi=mod(yi,boxysize) + if (yi.lt.0) yi=yi+boxysize + zi=mod(zi,boxzsize) + if (zi.lt.0) zi=zi+boxzsize + if ((zi.gt.bordlipbot) + &.and.(zi.lt.bordliptop)) then +C the energy transfer exist + if (zi.lt.buflipbot) then +C what fraction I am in + fracinbuf=1.0d0- + & ((zi-bordlipbot)/lipbufthick) +C lipbufthick is thickenes of lipid buffore + sslipi=sscalelip(fracinbuf) + ssgradlipi=-sscagradlip(fracinbuf)/lipbufthick + elseif (zi.gt.bufliptop) then + fracinbuf=1.0d0-((bordliptop-zi)/lipbufthick) + sslipi=sscalelip(fracinbuf) + ssgradlipi=sscagradlip(fracinbuf)/lipbufthick + else + sslipi=1.0d0 + ssgradlipi=0.0 + endif + else + sslipi=0.0d0 + ssgradlipi=0.0 + endif + dxi=dc_norm(1,nres+i) dyi=dc_norm(2,nres+i) dzi=dc_norm(3,nres+i) @@ -776,9 +1010,29 @@ 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 +C write (iout,'(a6,2i5,0pf7.3,a3,2f10.3)') +C & 'evdw',i,j,evdwij,' ss',evdw,evdw_t +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 +C write (iout,'(a6,2i5,0pf7.3,a3,2f10.3)') +C & 'evdw',i,j,evdwij,'tss',evdw,evdw_t + endif!dyn_ss_mask(k) + enddo! k + ELSE ind=ind+1 - itypj=itype(j) - if (itypj.eq.21) cycle + itypj=iabs(itype(j)) + if (itypj.eq.ntyp1) cycle dscj_inv=vbld_inv(j+nres) sig0ij=sigma(itypi,itypj) chi1=chi(itypi,itypj) @@ -800,17 +1054,96 @@ c chip12=0.0D0 c alf1=0.0D0 c alf2=0.0D0 c alf12=0.0D0 - xj=c(1,nres+j)-xi - yj=c(2,nres+j)-yi - zj=c(3,nres+j)-zi + xj=c(1,nres+j) + yj=c(2,nres+j) + zj=c(3,nres+j) +C returning jth atom to box + xj=mod(xj,boxxsize) + if (xj.lt.0) xj=xj+boxxsize + yj=mod(yj,boxysize) + if (yj.lt.0) yj=yj+boxysize + zj=mod(zj,boxzsize) + if (zj.lt.0) zj=zj+boxzsize + if ((zj.gt.bordlipbot) + &.and.(zj.lt.bordliptop)) then +C the energy transfer exist + if (zj.lt.buflipbot) then +C what fraction I am in + fracinbuf=1.0d0- + & ((zj-bordlipbot)/lipbufthick) +C lipbufthick is thickenes of lipid buffore + sslipj=sscalelip(fracinbuf) + ssgradlipj=-sscagradlip(fracinbuf)/lipbufthick + elseif (zj.gt.bufliptop) then + fracinbuf=1.0d0-((bordliptop-zj)/lipbufthick) + sslipj=sscalelip(fracinbuf) + ssgradlipj=sscagradlip(fracinbuf)/lipbufthick + else + sslipj=1.0d0 + ssgradlipj=0.0 + endif + else + sslipj=0.0d0 + ssgradlipj=0.0 + endif + aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 + & +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0 + bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 + & +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0 +C if (aa.ne.aa_aq(itypi,itypj)) then + +C write(iout,*) "tu,", i,j,aa_aq(itypi,itypj)-aa, +C & bb_aq(itypi,itypj)-bb, +C & sslipi,sslipj +C endif + +C write(iout,*),aa,aa_lip(itypi,itypj),aa_aq(itypi,itypj) +C checking the distance + dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2 + xj_safe=xj + yj_safe=yj + zj_safe=zj + subchap=0 +C finding the closest + do xshift=-1,1 + do yshift=-1,1 + do zshift=-1,1 + xj=xj_safe+xshift*boxxsize + yj=yj_safe+yshift*boxysize + zj=zj_safe+zshift*boxzsize + dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2 + if(dist_temp.lt.dist_init) then + dist_init=dist_temp + xj_temp=xj + yj_temp=yj + zj_temp=zj + subchap=1 + endif + enddo + enddo + enddo + if (subchap.eq.1) then + xj=xj_temp-xi + yj=yj_temp-yi + zj=zj_temp-zi + else + xj=xj_safe-xi + yj=yj_safe-yi + zj=zj_safe-zi + endif + dxj=dc_norm(1,nres+j) dyj=dc_norm(2,nres+j) dzj=dc_norm(3,nres+j) c write (iout,*) i,j,xj,yj,zj rrij=1.0D0/(xj*xj+yj*yj+zj*zj) rij=dsqrt(rrij) + sss=sscale((1.0d0/rij)/sigma(itypi,itypj)) + sssgrad=sscagrad((1.0d0/rij)/sigma(itypi,itypj)) + if (sss.le.0.0) cycle C Calculate angle-dependent terms of energy and contributions to their C derivatives. + call sc_angular sigsq=1.0D0/sigsq sig=sig0ij*dsqrt(sigsq) @@ -824,32 +1157,39 @@ C I hate to put IF's in the loops, but here don't have another choice!!!! c--------------------------------------------------------------- rij_shift=1.0D0/rij_shift fac=rij_shift**expon - e1=fac*fac*aa(itypi,itypj) - e2=fac*bb(itypi,itypj) + e1=fac*fac*aa + e2=fac*bb evdwij=eps1*eps2rt*eps3rt*(e1+e2) eps2der=evdwij*eps3rt eps3der=evdwij*eps2rt evdwij=evdwij*eps2rt*eps3rt - if (bb(itypi,itypj).gt.0) then - evdw=evdw+evdwij + if (bb.gt.0) then + evdw=evdw+evdwij*sss else - evdw_t=evdw_t+evdwij + evdw_t=evdw_t+evdwij*sss endif ij=icant(itypi,itypj) aux=eps1*eps2rt**2*eps3rt**2 +c eneps_temp(1,ij)=eneps_temp(1,ij)+aux*e1 +c & /dabs(eps(itypi,itypj)) +c eneps_temp(2,ij)=eneps_temp(2,ij)+aux*e2/eps(itypi,itypj) c write (iout,*) "i",i," j",j," itypi",itypi," itypj",itypj, c & " ij",ij," eneps",aux*e1/dabs(eps(itypi,itypj)), c & aux*e2/eps(itypi,itypj) c if (lprn) then - sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0) - epsi=bb(itypi,itypj)**2/aa(itypi,itypj) -c write (iout,'(2(a3,i3,2x),17(0pf7.3))') -c & restyp(itypi),i,restyp(itypj),j, -c & epsi,sigm,chi1,chi2,chip1,chip2, -c & eps1,eps2rt**2,eps3rt**2,sig,sig0ij, -c & om1,om2,om12,1.0D0/rij,1.0D0/rij_shift, -c & evdwij -c write (iout,*) "pratial sum", evdw,evdw_t + sigm=dabs(aa/bb)**(1.0D0/6.0D0) + epsi=bb**2/aa +C#define DEBUG +#ifdef DEBUG + write (iout,'(2(a3,i3,2x),17(0pf7.3))') + & restyp(itypi),i,restyp(itypj),j, + & epsi,sigm,chi1,chi2,chip1,chip2, + & eps1,eps2rt**2,eps3rt**2,sig,sig0ij, + & om1,om2,om12,1.0D0/rij,1.0D0/rij_shift, + & evdwij + write (iout,*) "partial sum", evdw, evdw_t +#endif +C#undef DEBUG c endif if (calc_grad) then C Calculate gradient components. @@ -857,6 +1197,7 @@ C Calculate gradient components. fac=-expon*(e1+evdwij)*rij_shift sigder=fac*sigder fac=rij*fac + fac=fac+evdwij/sss*sssgrad/sigma(itypi,itypj)*rij C Calculate the radial part of the gradient gg(1)=xj*fac gg(2)=yj*fac @@ -864,6 +1205,8 @@ C Calculate the radial part of the gradient C Calculate angular part of the gradient. call sc_grad endif +C write(iout,*) "partial sum", evdw, evdw_t + ENDIF ! dyn_ss enddo ! j enddo ! iint enddo ! i @@ -877,8 +1220,8 @@ C assuming the Gay-Berne-Vorobjev potential of interaction. C implicit real*8 (a-h,o-z) include 'DIMENSIONS' - include 'sizesclu.dat' include "DIMENSIONS.COMPAR" + include 'COMMON.CONTROL' include 'COMMON.GEO' include 'COMMON.VAR' include 'COMMON.LOCAL' @@ -888,10 +1231,16 @@ C include 'COMMON.INTERACT' include 'COMMON.IOUNITS' include 'COMMON.CALC' + include 'COMMON.SBRIDGE' common /srutu/ icall logical lprn integer icant external icant +c do i=1,210 +c do j=1,2 +c eneps_temp(j,i)=0.0d0 +c enddo +c enddo evdw=0.0D0 evdw_t=0.0d0 c print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon @@ -900,12 +1249,45 @@ c print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon c if (icall.gt.0) lprn=.true. ind=0 do i=iatsc_s,iatsc_e - itypi=itype(i) - if (itypi.eq.21) cycle - 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) +C returning the ith atom to box + xi=mod(xi,boxxsize) + if (xi.lt.0) xi=xi+boxxsize + yi=mod(yi,boxysize) + if (yi.lt.0) yi=yi+boxysize + zi=mod(zi,boxzsize) + if (zi.lt.0) zi=zi+boxzsize + if ((zi.gt.bordlipbot) + & .and.(zi.lt.bordliptop)) then +C the energy transfer exist + if (zi.lt.buflipbot) then +C what fraction I am in + fracinbuf=1.0d0- + & ((zi-bordlipbot)/lipbufthick) +C lipbufthick is thickenes of lipid buffore + sslipi=sscalelip(fracinbuf) + ssgradlipi=-sscagradlip(fracinbuf)/lipbufthick + elseif (zi.gt.bufliptop) then + fracinbuf=1.0d0-((bordliptop-zi)/lipbufthick) + sslipi=sscalelip(fracinbuf) + ssgradlipi=sscagradlip(fracinbuf)/lipbufthick + else + sslipi=1.0d0 + ssgradlipi=0.0 + endif + else + sslipi=0.0d0 + ssgradlipi=0.0 + endif + dxi=dc_norm(1,nres+i) + dyi=dc_norm(2,nres+i) + dzi=dc_norm(3,nres+i) + dsci_inv=vbld_inv(i+nres) dxi=dc_norm(1,nres+i) dyi=dc_norm(2,nres+i) dzi=dc_norm(3,nres+i) @@ -915,9 +1297,29 @@ 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,a3,2f10.3)') + & 'evdw',i,j,evdwij,' ss',evdw,evdw_t +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,a3,2f10.3)') + & 'evdw',i,j,evdwij,'tss',evdw,evdw_t + endif!dyn_ss_mask(k) + enddo! k + ELSE ind=ind+1 - itypj=itype(j) - if (itypj.eq.21) cycle + itypj=iabs(itype(j)) + if (itypj.eq.ntyp1) cycle dscj_inv=vbld_inv(j+nres) sig0ij=sigma(itypi,itypj) r0ij=r0(itypi,itypj) @@ -940,16 +1342,96 @@ c chip12=0.0D0 c alf1=0.0D0 c alf2=0.0D0 c alf12=0.0D0 - xj=c(1,nres+j)-xi - yj=c(2,nres+j)-yi - zj=c(3,nres+j)-zi + xj=c(1,nres+j) + yj=c(2,nres+j) + zj=c(3,nres+j) +C returning jth atom to box + xj=mod(xj,boxxsize) + if (xj.lt.0) xj=xj+boxxsize + yj=mod(yj,boxysize) + if (yj.lt.0) yj=yj+boxysize + zj=mod(zj,boxzsize) + if (zj.lt.0) zj=zj+boxzsize + if ((zj.gt.bordlipbot) + & .and.(zj.lt.bordliptop)) then +C the energy transfer exist + if (zj.lt.buflipbot) then +C what fraction I am in + fracinbuf=1.0d0- + & ((zj-bordlipbot)/lipbufthick) +C lipbufthick is thickenes of lipid buffore + sslipj=sscalelip(fracinbuf) + ssgradlipj=-sscagradlip(fracinbuf)/lipbufthick + elseif (zj.gt.bufliptop) then + fracinbuf=1.0d0-((bordliptop-zj)/lipbufthick) + sslipj=sscalelip(fracinbuf) + ssgradlipj=sscagradlip(fracinbuf)/lipbufthick + else + sslipj=1.0d0 + ssgradlipj=0.0 + endif + else + sslipj=0.0d0 + ssgradlipj=0.0 + endif + aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 + & +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0 + bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 + & +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0 +C if (aa.ne.aa_aq(itypi,itypj)) then + +C write(iout,*) "tu,", i,j,aa_aq(itypi,itypj)-aa, +C & bb_aq(itypi,itypj)-bb, +C & sslipi,sslipj +C endif + +C write(iout,*),aa,aa_lip(itypi,itypj),aa_aq(itypi,itypj) +C checking the distance + dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2 + xj_safe=xj + yj_safe=yj + zj_safe=zj + subchap=0 +C finding the closest + do xshift=-1,1 + do yshift=-1,1 + do zshift=-1,1 + xj=xj_safe+xshift*boxxsize + yj=yj_safe+yshift*boxysize + zj=zj_safe+zshift*boxzsize + dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2 + if (dist_temp.lt.dist_init) then + dist_init=dist_temp + xj_temp=xj + yj_temp=yj + zj_temp=zj + subchap=1 + endif + enddo + enddo + enddo + if (subchap.eq.1) then + xj=xj_temp-xi + yj=yj_temp-yi + zj=zj_temp-zi + else + xj=xj_safe-xi + yj=yj_safe-yi + zj=zj_safe-zi + endif + dxj=dc_norm(1,nres+j) dyj=dc_norm(2,nres+j) dzj=dc_norm(3,nres+j) +c write (iout,*) i,j,xj,yj,zj rrij=1.0D0/(xj*xj+yj*yj+zj*zj) rij=dsqrt(rrij) + sss=sscale((1.0d0/rij)/sigma(itypi,itypj)) + sssgrad=sscagrad((1.0d0/rij)/sigma(itypi,itypj)) + if (sss.le.0.0) cycle C Calculate angle-dependent terms of energy and contributions to their C derivatives. + call sc_angular sigsq=1.0D0/sigsq sig=sig0ij*dsqrt(sigsq) @@ -963,38 +1445,53 @@ C I hate to put IF's in the loops, but here don't have another choice!!!! c--------------------------------------------------------------- rij_shift=1.0D0/rij_shift fac=rij_shift**expon - e1=fac*fac*aa(itypi,itypj) - e2=fac*bb(itypi,itypj) + e1=fac*fac*aa + e2=fac*bb evdwij=eps1*eps2rt*eps3rt*(e1+e2) eps2der=evdwij*eps3rt eps3der=evdwij*eps2rt fac_augm=rrij**expon e_augm=augm(itypi,itypj)*fac_augm evdwij=evdwij*eps2rt*eps3rt - if (bb(itypi,itypj).gt.0.0d0) then - evdw=evdw+evdwij+e_augm + if (bb.gt.0) then + evdw=evdw+evdwij*sss+e_augm else - evdw_t=evdw_t+evdwij+e_augm + evdw_t=evdw_t+evdwij*sss+e_augm endif +c evdw=evdw+evdwij+e_augm ij=icant(itypi,itypj) aux=eps1*eps2rt**2*eps3rt**2 +c eneps_temp(1,ij)=eneps_temp(1,ij)+aux*e1 +c & /dabs(eps(itypi,itypj)) +c eneps_temp(2,ij)=eneps_temp(2,ij)+aux*e2/eps(itypi,itypj) +c write (iout,*) "i",i," j",j," itypi",itypi," itypj",itypj, +c & " ij",ij," eneps",aux*e1/dabs(eps(itypi,itypj)), +c & aux*e2/eps(itypi,itypj) c if (lprn) then -c sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0) -c epsi=bb(itypi,itypj)**2/aa(itypi,itypj) -c write (iout,'(2(a3,i3,2x),17(0pf7.3))') -c & restyp(itypi),i,restyp(itypj),j, -c & epsi,sigm,sig,(augm(itypi,itypj)/epsi)**(1.0D0/12.0D0), -c & chi1,chi2,chip1,chip2, -c & eps1,eps2rt**2,eps3rt**2, -c & om1,om2,om12,1.0D0/rij,1.0D0/rij_shift, -c & evdwij+e_augm +c#define DEBUG +#ifdef DEBUG + sigm=dabs(aa/bb)**(1.0D0/6.0D0) + epsi=bb**2/aa + write (iout,'(2(a3,i3,2x),17(0pf7.3))') + & restyp(itypi),i,restyp(itypj),j, + & epsi,sigm,sig,(augm(itypi,itypj)/epsi)**(1.0D0/12.0D0), + & chi1,chi2,chip1,chip2, + & eps1,eps2rt**2,eps3rt**2, + & om1,om2,om12,1.0D0/rij,1.0D0/rij_shift, + & evdwij+e_augm + write (iout,*) "partial sum", evdw, evdw_t +#endif +c#undef DEBUG c endif + if (energy_dec) write (iout,'(a6,2i5,0pf7.3)') + & 'evdw',i,j,evdwij if (calc_grad) then C Calculate gradient components. e1=e1*eps1*eps2rt**2*eps3rt**2 fac=-expon*(e1+evdwij)*rij_shift sigder=fac*sigder - fac=rij*fac-2*expon*rrij*e_augm + fac=rij*fac + fac=fac+evdwij/sss*sssgrad/sigma(itypi,itypj)*rij C Calculate the radial part of the gradient gg(1)=xj*fac gg(2)=yj*fac @@ -1002,6 +1499,7 @@ C Calculate the radial part of the gradient C Calculate angular part of the gradient. call sc_grad endif + ENDIF enddo ! j enddo ! iint enddo ! i @@ -1060,7 +1558,6 @@ C---------------------------------------------------------------------------- subroutine sc_grad implicit real*8 (a-h,o-z) include 'DIMENSIONS' - include 'sizesclu.dat' include 'COMMON.CHAIN' include 'COMMON.DERIV' include 'COMMON.CALC' @@ -1098,7 +1595,6 @@ c------------------------------------------------------------------------------ subroutine vec_and_deriv implicit real*8 (a-h,o-z) include 'DIMENSIONS' - include 'sizesclu.dat' include 'COMMON.IOUNITS' include 'COMMON.GEO' include 'COMMON.VAR' @@ -1119,6 +1615,8 @@ C Compute the Z-axis call vecpr(dc_norm(1,i),dc_norm(1,i-1),uz(1,i)) costh=dcos(pi-theta(nres)) fac=1.0d0/dsqrt(1.0d0-costh*costh) +c write (iout,*) "i",i," dc_norm",dc_norm(:,i),dc_norm(:,i-1), +c & " uz",uz(:,i) do k=1,3 uz(k,i)=fac*uz(k,i) enddo @@ -1142,7 +1640,7 @@ C Compute the derivatives of uz uzder(1,3,2)= dc_norm(2,i) uzder(2,3,2)=-dc_norm(1,i) uzder(3,3,2)= 0.0d0 - endif + endif ! calc_grad C Compute the Y-axis facy=fac do k=1,3 @@ -1253,288 +1751,24 @@ C Compute the derivatives of uy endif return end -C----------------------------------------------------------------------------- - subroutine vec_and_deriv_test +C-------------------------------------------------------------------------- + subroutine set_matrices implicit real*8 (a-h,o-z) include 'DIMENSIONS' - include 'sizesclu.dat' +#ifdef MPI + include "mpif.h" + integer IERR + integer status(MPI_STATUS_SIZE) +#endif include 'COMMON.IOUNITS' include 'COMMON.GEO' include 'COMMON.VAR' include 'COMMON.LOCAL' include 'COMMON.CHAIN' - include 'COMMON.VECTORS' - dimension uyder(3,3,2),uzder(3,3,2) -C Compute the local reference systems. For reference system (i), the -C X-axis points from CA(i) to CA(i+1), the Y axis is in the -C CA(i)-CA(i+1)-CA(i+2) plane, and the Z axis is perpendicular to this plane. - do i=1,nres-1 - if (i.eq.nres-1) then -C Case of the last full residue -C Compute the Z-axis - call vecpr(dc_norm(1,i),dc_norm(1,i-1),uz(1,i)) - costh=dcos(pi-theta(nres)) - fac=1.0d0/dsqrt(1.0d0-costh*costh) -c write (iout,*) 'fac',fac, -c & 1.0d0/dsqrt(scalar(uz(1,i),uz(1,i))) - fac=1.0d0/dsqrt(scalar(uz(1,i),uz(1,i))) - do k=1,3 - uz(k,i)=fac*uz(k,i) - enddo -C Compute the derivatives of uz - uzder(1,1,1)= 0.0d0 - uzder(2,1,1)=-dc_norm(3,i-1) - uzder(3,1,1)= dc_norm(2,i-1) - uzder(1,2,1)= dc_norm(3,i-1) - uzder(2,2,1)= 0.0d0 - uzder(3,2,1)=-dc_norm(1,i-1) - uzder(1,3,1)=-dc_norm(2,i-1) - uzder(2,3,1)= dc_norm(1,i-1) - uzder(3,3,1)= 0.0d0 - uzder(1,1,2)= 0.0d0 - uzder(2,1,2)= dc_norm(3,i) - uzder(3,1,2)=-dc_norm(2,i) - uzder(1,2,2)=-dc_norm(3,i) - uzder(2,2,2)= 0.0d0 - uzder(3,2,2)= dc_norm(1,i) - uzder(1,3,2)= dc_norm(2,i) - uzder(2,3,2)=-dc_norm(1,i) - uzder(3,3,2)= 0.0d0 -C Compute the Y-axis - do k=1,3 - uy(k,i)=fac*(dc_norm(k,i-1)-costh*dc_norm(k,i)) - enddo - facy=fac - facy=1.0d0/dsqrt(scalar(dc_norm(1,i),dc_norm(1,i))* - & (scalar(dc_norm(1,i-1),dc_norm(1,i-1))**2- - & scalar(dc_norm(1,i),dc_norm(1,i-1))**2)) - do k=1,3 -c uy(k,i)=facy*(dc_norm(k,i+1)-costh*dc_norm(k,i)) - uy(k,i)= -c & facy*( - & dc_norm(k,i-1)*scalar(dc_norm(1,i),dc_norm(1,i)) - & -scalar(dc_norm(1,i),dc_norm(1,i-1))*dc_norm(k,i) -c & ) - enddo -c write (iout,*) 'facy',facy, -c & 1.0d0/dsqrt(scalar(uy(1,i),uy(1,i))) - facy=1.0d0/dsqrt(scalar(uy(1,i),uy(1,i))) - do k=1,3 - uy(k,i)=facy*uy(k,i) - enddo -C Compute the derivatives of uy - do j=1,3 - do k=1,3 - uyder(k,j,1)=2*dc_norm(k,i-1)*dc_norm(j,i) - & -dc_norm(k,i)*dc_norm(j,i-1) - uyder(k,j,2)=-dc_norm(j,i)*dc_norm(k,i) - enddo -c uyder(j,j,1)=uyder(j,j,1)-costh -c uyder(j,j,2)=1.0d0+uyder(j,j,2) - uyder(j,j,1)=uyder(j,j,1) - & -scalar(dc_norm(1,i),dc_norm(1,i-1)) - uyder(j,j,2)=scalar(dc_norm(1,i),dc_norm(1,i)) - & +uyder(j,j,2) - enddo - do j=1,2 - do k=1,3 - do l=1,3 - uygrad(l,k,j,i)=uyder(l,k,j) - uzgrad(l,k,j,i)=uzder(l,k,j) - enddo - enddo - enddo - call unormderiv(uy(1,i),uyder(1,1,1),facy,uygrad(1,1,1,i)) - call unormderiv(uy(1,i),uyder(1,1,2),facy,uygrad(1,1,2,i)) - call unormderiv(uz(1,i),uzder(1,1,1),fac,uzgrad(1,1,1,i)) - call unormderiv(uz(1,i),uzder(1,1,2),fac,uzgrad(1,1,2,i)) - else -C Other residues -C Compute the Z-axis - call vecpr(dc_norm(1,i),dc_norm(1,i+1),uz(1,i)) - costh=dcos(pi-theta(i+2)) - fac=1.0d0/dsqrt(1.0d0-costh*costh) - fac=1.0d0/dsqrt(scalar(uz(1,i),uz(1,i))) - do k=1,3 - uz(k,i)=fac*uz(k,i) - enddo -C Compute the derivatives of uz - uzder(1,1,1)= 0.0d0 - uzder(2,1,1)=-dc_norm(3,i+1) - uzder(3,1,1)= dc_norm(2,i+1) - uzder(1,2,1)= dc_norm(3,i+1) - uzder(2,2,1)= 0.0d0 - uzder(3,2,1)=-dc_norm(1,i+1) - uzder(1,3,1)=-dc_norm(2,i+1) - uzder(2,3,1)= dc_norm(1,i+1) - uzder(3,3,1)= 0.0d0 - uzder(1,1,2)= 0.0d0 - uzder(2,1,2)= dc_norm(3,i) - uzder(3,1,2)=-dc_norm(2,i) - uzder(1,2,2)=-dc_norm(3,i) - uzder(2,2,2)= 0.0d0 - uzder(3,2,2)= dc_norm(1,i) - uzder(1,3,2)= dc_norm(2,i) - uzder(2,3,2)=-dc_norm(1,i) - uzder(3,3,2)= 0.0d0 -C Compute the Y-axis - facy=fac - facy=1.0d0/dsqrt(scalar(dc_norm(1,i),dc_norm(1,i))* - & (scalar(dc_norm(1,i+1),dc_norm(1,i+1))**2- - & scalar(dc_norm(1,i),dc_norm(1,i+1))**2)) - do k=1,3 -c uy(k,i)=facy*(dc_norm(k,i+1)-costh*dc_norm(k,i)) - uy(k,i)= -c & facy*( - & dc_norm(k,i+1)*scalar(dc_norm(1,i),dc_norm(1,i)) - & -scalar(dc_norm(1,i),dc_norm(1,i+1))*dc_norm(k,i) -c & ) - enddo -c write (iout,*) 'facy',facy, -c & 1.0d0/dsqrt(scalar(uy(1,i),uy(1,i))) - facy=1.0d0/dsqrt(scalar(uy(1,i),uy(1,i))) - do k=1,3 - uy(k,i)=facy*uy(k,i) - enddo -C Compute the derivatives of uy - do j=1,3 - do k=1,3 - uyder(k,j,1)=2*dc_norm(k,i+1)*dc_norm(j,i) - & -dc_norm(k,i)*dc_norm(j,i+1) - uyder(k,j,2)=-dc_norm(j,i)*dc_norm(k,i) - enddo -c uyder(j,j,1)=uyder(j,j,1)-costh -c uyder(j,j,2)=1.0d0+uyder(j,j,2) - uyder(j,j,1)=uyder(j,j,1) - & -scalar(dc_norm(1,i),dc_norm(1,i+1)) - uyder(j,j,2)=scalar(dc_norm(1,i),dc_norm(1,i)) - & +uyder(j,j,2) - enddo - do j=1,2 - do k=1,3 - do l=1,3 - uygrad(l,k,j,i)=uyder(l,k,j) - uzgrad(l,k,j,i)=uzder(l,k,j) - enddo - enddo - enddo - call unormderiv(uy(1,i),uyder(1,1,1),facy,uygrad(1,1,1,i)) - call unormderiv(uy(1,i),uyder(1,1,2),facy,uygrad(1,1,2,i)) - call unormderiv(uz(1,i),uzder(1,1,1),fac,uzgrad(1,1,1,i)) - call unormderiv(uz(1,i),uzder(1,1,2),fac,uzgrad(1,1,2,i)) - endif - enddo - do i=1,nres-1 - do j=1,2 - do k=1,3 - do l=1,3 - uygrad(l,k,j,i)=vblinv*uygrad(l,k,j,i) - uzgrad(l,k,j,i)=vblinv*uzgrad(l,k,j,i) - enddo - enddo - enddo - enddo - return - end -C----------------------------------------------------------------------------- - subroutine check_vecgrad - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' - include 'sizesclu.dat' - include 'COMMON.IOUNITS' - include 'COMMON.GEO' - include 'COMMON.VAR' - include 'COMMON.LOCAL' - include 'COMMON.CHAIN' - include 'COMMON.VECTORS' - dimension uygradt(3,3,2,maxres),uzgradt(3,3,2,maxres) - dimension uyt(3,maxres),uzt(3,maxres) - dimension uygradn(3,3,2),uzgradn(3,3,2),erij(3) - double precision delta /1.0d-7/ - call vec_and_deriv -cd do i=1,nres -crc write(iout,'(2i5,2(3f10.5,5x))') i,1,dc_norm(:,i) -crc write(iout,'(2i5,2(3f10.5,5x))') i,2,uy(:,i) -crc write(iout,'(2i5,2(3f10.5,5x)/)')i,3,uz(:,i) -cd write(iout,'(2i5,2(3f10.5,5x))') i,1, -cd & (dc_norm(if90,i),if90=1,3) -cd write(iout,'(2i5,2(3f10.5,5x))') i,2,(uy(if90,i),if90=1,3) -cd write(iout,'(2i5,2(3f10.5,5x)/)')i,3,(uz(if90,i),if90=1,3) -cd write(iout,'(a)') -cd enddo - do i=1,nres - do j=1,2 - do k=1,3 - do l=1,3 - uygradt(l,k,j,i)=uygrad(l,k,j,i) - uzgradt(l,k,j,i)=uzgrad(l,k,j,i) - enddo - enddo - enddo - enddo - call vec_and_deriv - do i=1,nres - do j=1,3 - uyt(j,i)=uy(j,i) - uzt(j,i)=uz(j,i) - enddo - enddo - do i=1,nres -cd write (iout,*) 'i=',i - do k=1,3 - erij(k)=dc_norm(k,i) - enddo - do j=1,3 - do k=1,3 - dc_norm(k,i)=erij(k) - enddo - dc_norm(j,i)=dc_norm(j,i)+delta -c fac=dsqrt(scalar(dc_norm(1,i),dc_norm(1,i))) -c do k=1,3 -c dc_norm(k,i)=dc_norm(k,i)/fac -c enddo -c write (iout,*) (dc_norm(k,i),k=1,3) -c write (iout,*) (erij(k),k=1,3) - call vec_and_deriv - do k=1,3 - uygradn(k,j,1)=(uy(k,i)-uyt(k,i))/delta - uygradn(k,j,2)=(uy(k,i-1)-uyt(k,i-1))/delta - uzgradn(k,j,1)=(uz(k,i)-uzt(k,i))/delta - uzgradn(k,j,2)=(uz(k,i-1)-uzt(k,i-1))/delta - enddo -c write (iout,'(i5,3f8.5,3x,3f8.5,5x,3f8.5,3x,3f8.5)') -c & j,(uzgradt(k,j,1,i),k=1,3),(uzgradn(k,j,1),k=1,3), -c & (uzgradt(k,j,2,i-1),k=1,3),(uzgradn(k,j,2),k=1,3) - enddo - do k=1,3 - dc_norm(k,i)=erij(k) - enddo -cd do k=1,3 -cd write (iout,'(i5,3f8.5,3x,3f8.5,5x,3f8.5,3x,3f8.5)') -cd & k,(uygradt(k,l,1,i),l=1,3),(uygradn(k,l,1),l=1,3), -cd & (uygradt(k,l,2,i-1),l=1,3),(uygradn(k,l,2),l=1,3) -cd write (iout,'(i5,3f8.5,3x,3f8.5,5x,3f8.5,3x,3f8.5)') -cd & k,(uzgradt(k,l,1,i),l=1,3),(uzgradn(k,l,1),l=1,3), -cd & (uzgradt(k,l,2,i-1),l=1,3),(uzgradn(k,l,2),l=1,3) -cd write (iout,'(a)') -cd enddo - enddo - return - end -C-------------------------------------------------------------------------- - subroutine set_matrices - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' - include 'sizesclu.dat' - include 'COMMON.IOUNITS' - include 'COMMON.GEO' - include 'COMMON.VAR' - include 'COMMON.LOCAL' - include 'COMMON.CHAIN' - include 'COMMON.DERIV' - include 'COMMON.INTERACT' - include 'COMMON.CONTACTS' - include 'COMMON.TORSION' + include 'COMMON.DERIV' + include 'COMMON.INTERACT' + include 'COMMON.CONTACTS' + include 'COMMON.TORSION' include 'COMMON.VECTORS' include 'COMMON.FFIELD' double precision auxvec(2),auxmat(2,2) @@ -1542,6 +1776,130 @@ C C Compute the virtual-bond-torsional-angle dependent quantities needed C to calculate the el-loc multibody terms of various order. C +c write(iout,*) 'SET_MATRICES nphi=',nphi,nres + do i=3,nres+1 + if (i.gt. nnt+2 .and. i.lt.nct+2) then + iti = itype2loc(itype(i-2)) + else + iti=nloctyp + endif +c if (i.gt. iatel_s+1 .and. i.lt.iatel_e+4) then + if (i.gt. nnt+1 .and. i.lt.nct+1) then + iti1 = itype2loc(itype(i-1)) + else + iti1=nloctyp + endif +#ifdef NEWCORR + cost1=dcos(theta(i-1)) + sint1=dsin(theta(i-1)) + sint1sq=sint1*sint1 + sint1cub=sint1sq*sint1 + sint1cost1=2*sint1*cost1 +#ifdef DEBUG + write (iout,*) "bnew1",i,iti + write (iout,*) (bnew1(k,1,iti),k=1,3) + write (iout,*) (bnew1(k,2,iti),k=1,3) + write (iout,*) "bnew2",i,iti + write (iout,*) (bnew2(k,1,iti),k=1,3) + write (iout,*) (bnew2(k,2,iti),k=1,3) +#endif + do k=1,2 + b1k=bnew1(1,k,iti)+(bnew1(2,k,iti)+bnew1(3,k,iti)*cost1)*cost1 + b1(k,i-2)=sint1*b1k + gtb1(k,i-2)=cost1*b1k-sint1sq* + & (bnew1(2,k,iti)+2*bnew1(3,k,iti)*cost1) + b2k=bnew2(1,k,iti)+(bnew2(2,k,iti)+bnew2(3,k,iti)*cost1)*cost1 + b2(k,i-2)=sint1*b2k + if (calc_grad) gtb2(k,i-2)=cost1*b2k-sint1sq* + & (bnew2(2,k,iti)+2*bnew2(3,k,iti)*cost1) + enddo + do k=1,2 + aux=ccnew(1,k,iti)+(ccnew(2,k,iti)+ccnew(3,k,iti)*cost1)*cost1 + cc(1,k,i-2)=sint1sq*aux + if (calc_grad) gtcc(1,k,i-2)=sint1cost1*aux-sint1cub* + & (ccnew(2,k,iti)+2*ccnew(3,k,iti)*cost1) + aux=ddnew(1,k,iti)+(ddnew(2,k,iti)+ddnew(3,k,iti)*cost1)*cost1 + dd(1,k,i-2)=sint1sq*aux + if (calc_grad) gtdd(1,k,i-2)=sint1cost1*aux-sint1cub* + & (ddnew(2,k,iti)+2*ddnew(3,k,iti)*cost1) + enddo + cc(2,1,i-2)=cc(1,2,i-2) + cc(2,2,i-2)=-cc(1,1,i-2) + gtcc(2,1,i-2)=gtcc(1,2,i-2) + gtcc(2,2,i-2)=-gtcc(1,1,i-2) + dd(2,1,i-2)=dd(1,2,i-2) + dd(2,2,i-2)=-dd(1,1,i-2) + gtdd(2,1,i-2)=gtdd(1,2,i-2) + gtdd(2,2,i-2)=-gtdd(1,1,i-2) + do k=1,2 + do l=1,2 + aux=eenew(1,l,k,iti)+eenew(2,l,k,iti)*cost1 + EE(l,k,i-2)=sint1sq*aux + if (calc_grad) + & gtEE(l,k,i-2)=sint1cost1*aux-sint1cub*eenew(2,l,k,iti) + enddo + enddo + EE(1,1,i-2)=EE(1,1,i-2)+e0new(1,iti)*cost1 + EE(1,2,i-2)=EE(1,2,i-2)+e0new(2,iti)+e0new(3,iti)*cost1 + EE(2,1,i-2)=EE(2,1,i-2)+e0new(2,iti)*cost1+e0new(3,iti) + EE(2,2,i-2)=EE(2,2,i-2)-e0new(1,iti) + if (calc_grad) then + gtEE(1,1,i-2)=gtEE(1,1,i-2)-e0new(1,iti)*sint1 + gtEE(1,2,i-2)=gtEE(1,2,i-2)-e0new(3,iti)*sint1 + gtEE(2,1,i-2)=gtEE(2,1,i-2)-e0new(2,iti)*sint1 + endif +c b1tilde(1,i-2)=b1(1,i-2) +c b1tilde(2,i-2)=-b1(2,i-2) +c b2tilde(1,i-2)=b2(1,i-2) +c b2tilde(2,i-2)=-b2(2,i-2) +#ifdef DEBUG + write (iout,*) 'i=',i-2,gtb1(2,i-2),gtb1(1,i-2) + write(iout,*) 'b1=',(b1(k,i-2),k=1,2) + write(iout,*) 'b2=',(b2(k,i-2),k=1,2) + write (iout,*) 'theta=', theta(i-1) +#endif +#else +c if (i.gt. nnt+2 .and. i.lt.nct+2) then +c iti = itype2loc(itype(i-2)) +c else +c iti=nloctyp +c endif +c if (i.gt. iatel_s+1 .and. i.lt.iatel_e+4) then +c if (i.gt. nnt+1 .and. i.lt.nct+1) then +c iti1 = itype2loc(itype(i-1)) +c else +c iti1=nloctyp +c endif + b1(1,i-2)=b(3,iti) + b1(2,i-2)=b(5,iti) + b2(1,i-2)=b(2,iti) + b2(2,i-2)=b(4,iti) + do k=1,2 + do l=1,2 + CC(k,l,i-2)=ccold(k,l,iti) + DD(k,l,i-2)=ddold(k,l,iti) + EE(k,l,i-2)=eeold(k,l,iti) + enddo + enddo +#endif + b1tilde(1,i-2)= b1(1,i-2) + b1tilde(2,i-2)=-b1(2,i-2) + b2tilde(1,i-2)= b2(1,i-2) + b2tilde(2,i-2)=-b2(2,i-2) +c + Ctilde(1,1,i-2)= CC(1,1,i-2) + Ctilde(1,2,i-2)= CC(1,2,i-2) + Ctilde(2,1,i-2)=-CC(2,1,i-2) + Ctilde(2,2,i-2)=-CC(2,2,i-2) +c + Dtilde(1,1,i-2)= DD(1,1,i-2) + Dtilde(1,2,i-2)= DD(1,2,i-2) + Dtilde(2,1,i-2)=-DD(2,1,i-2) + Dtilde(2,2,i-2)=-DD(2,2,i-2) +c write(iout,*) "i",i," iti",iti +c write(iout,*) 'b1=',(b1(k,i-2),k=1,2) +c write(iout,*) 'b2=',(b2(k,i-2),k=1,2) + enddo do i=3,nres+1 if (i .lt. nres+1) then sin1=dsin(phi(i)) @@ -1609,37 +1967,44 @@ C Ug2der(2,1,i-2)=0.0d0 Ug2der(2,2,i-2)=0.0d0 endif +c if (i.gt. iatel_s+2 .and. i.lt.iatel_e+5) then if (i.gt. nnt+2 .and. i.lt.nct+2) then - if (itype(i-2).le.ntyp) then - iti = itortyp(itype(i-2)) - else - iti=ntortyp+1 - endif + iti = itype2loc(itype(i-2)) else - iti=ntortyp+1 + iti=nloctyp endif +c if (i.gt. iatel_s+1 .and. i.lt.iatel_e+4) then if (i.gt. nnt+1 .and. i.lt.nct+1) then - if (itype(i-1).le.ntyp) then - iti1 = itortyp(itype(i-1)) - else - iti1=ntortyp+1 - endif + iti1 = itype2loc(itype(i-1)) else - iti1=ntortyp+1 + iti1=nloctyp endif cd write (iout,*) '*******i',i,' iti1',iti cd write (iout,*) 'b1',b1(:,iti) cd write (iout,*) 'b2',b2(:,iti) cd write (iout,*) 'Ug',Ug(:,:,i-2) -c print *,"itilde1 i iti iti1",i,iti,iti1 - if (i .gt. iatel_s+2) then - call matvec2(Ug(1,1,i-2),b2(1,iti),Ub2(1,i-2)) - call matmat2(EE(1,1,iti),Ug(1,1,i-2),EUg(1,1,i-2)) - call matmat2(CC(1,1,iti),Ug(1,1,i-2),CUg(1,1,i-2)) - call matmat2(DD(1,1,iti),Ug(1,1,i-2),DUg(1,1,i-2)) - call matmat2(Dtilde(1,1,iti),Ug2(1,1,i-2),DtUg2(1,1,i-2)) - call matvec2(Ctilde(1,1,iti1),obrot(1,i-2),Ctobr(1,i-2)) - call matvec2(Dtilde(1,1,iti),obrot2(1,i-2),Dtobr2(1,i-2)) +c if (i .gt. iatel_s+2) then + if (i .gt. nnt+2) then + call matvec2(Ug(1,1,i-2),b2(1,i-2),Ub2(1,i-2)) +#ifdef NEWCORR + call matvec2(Ug(1,1,i-2),gtb2(1,i-2),gUb2(1,i-2)) +c write (iout,*) Ug(1,1,i-2),gtb2(1,i-2),gUb2(1,i-2),"chuj" +#endif +c write(iout,*) "co jest kurwa", iti, EE(1,1,i),EE(2,1,i), +c & EE(1,2,iti),EE(2,2,i) + call matmat2(EE(1,1,i-2),Ug(1,1,i-2),EUg(1,1,i-2)) + call matmat2(gtEE(1,1,i-2),Ug(1,1,i-2),gtEUg(1,1,i-2)) +c write(iout,*) "Macierz EUG", +c & eug(1,1,i-2),eug(1,2,i-2),eug(2,1,i-2), +c & eug(2,2,i-2) + if (wcorr4.gt.0.0d0 .or. wcorr5.gt.0.0d0 .or. wcorr6.gt.0.0d0) + & then + call matmat2(CC(1,1,i-2),Ug(1,1,i-2),CUg(1,1,i-2)) + call matmat2(DD(1,1,i-2),Ug(1,1,i-2),DUg(1,1,i-2)) + call matmat2(Dtilde(1,1,i-2),Ug2(1,1,i-2),DtUg2(1,1,i-2)) + call matvec2(Ctilde(1,1,i-1),obrot(1,i-2),Ctobr(1,i-2)) + call matvec2(Dtilde(1,1,i-2),obrot2(1,i-2),Dtobr2(1,i-2)) + endif else do k=1,2 Ub2(k,i-2)=0.0d0 @@ -1653,63 +2018,76 @@ c print *,"itilde1 i iti iti1",i,iti,iti1 enddo enddo endif -c print *,"itilde2 i iti iti1",i,iti,iti1 - call matvec2(Ugder(1,1,i-2),b2(1,iti),Ub2der(1,i-2)) - call matmat2(EE(1,1,iti),Ugder(1,1,i-2),EUgder(1,1,i-2)) - call matmat2(CC(1,1,iti1),Ugder(1,1,i-2),CUgder(1,1,i-2)) - call matmat2(DD(1,1,iti),Ugder(1,1,i-2),DUgder(1,1,i-2)) - call matmat2(Dtilde(1,1,iti),Ug2der(1,1,i-2),DtUg2der(1,1,i-2)) - call matvec2(Ctilde(1,1,iti1),obrot_der(1,i-2),Ctobrder(1,i-2)) - call matvec2(Dtilde(1,1,iti),obrot2_der(1,i-2),Dtobr2der(1,i-2)) -c print *,"itilde3 i iti iti1",i,iti,iti1 + call matvec2(Ugder(1,1,i-2),b2(1,i-2),Ub2der(1,i-2)) + call matmat2(EE(1,1,i-2),Ugder(1,1,i-2),EUgder(1,1,i-2)) do k=1,2 muder(k,i-2)=Ub2der(k,i-2) enddo +c if (i.gt. iatel_s+1 .and. i.lt.iatel_e+4) then if (i.gt. nnt+1 .and. i.lt.nct+1) then if (itype(i-1).le.ntyp) then - iti1 = itortyp(itype(i-1)) + iti1 = itype2loc(itype(i-1)) else - iti1=ntortyp+1 + iti1=nloctyp endif else - iti1=ntortyp+1 + iti1=nloctyp endif do k=1,2 - mu(k,i-2)=Ub2(k,i-2)+b1(k,iti1) + mu(k,i-2)=Ub2(k,i-2)+b1(k,i-1) enddo +#ifdef MUOUT + write (iout,'(2hmu,i3,3f8.1,12f10.5)') i-2,rad2deg*theta(i-1), + & rad2deg*theta(i),rad2deg*phi(i),mu(1,i-2),mu(2,i-2), + & -b2(1,i-2),b2(2,i-2),b1(1,i-2),b1(2,i-2), + & dsqrt(b2(1,i-1)**2+b2(2,i-1)**2) + & +dsqrt(b1(1,i-1)**2+b1(2,i-1)**2), + & ((ee(l,k,i-2),l=1,2),k=1,2) +#endif +cd write (iout,*) 'mu1',mu1(:,i-2) +cd write (iout,*) 'mu2',mu2(:,i-2) + if (wcorr4.gt.0.0d0 .or. wcorr5.gt.0.0d0 .or.wcorr6.gt.0.0d0) + & then + if (calc_grad) then + call matmat2(CC(1,1,i-1),Ugder(1,1,i-2),CUgder(1,1,i-2)) + call matmat2(DD(1,1,i-2),Ugder(1,1,i-2),DUgder(1,1,i-2)) + call matmat2(Dtilde(1,1,i-2),Ug2der(1,1,i-2),DtUg2der(1,1,i-2)) + call matvec2(Ctilde(1,1,i-1),obrot_der(1,i-2),Ctobrder(1,i-2)) + call matvec2(Dtilde(1,1,i-2),obrot2_der(1,i-2),Dtobr2der(1,i-2)) + endif C Vectors and matrices dependent on a single virtual-bond dihedral. - call matvec2(DD(1,1,iti),b1tilde(1,iti1),auxvec(1)) + call matvec2(DD(1,1,i-2),b1tilde(1,i-1),auxvec(1)) call matvec2(Ug2(1,1,i-2),auxvec(1),Ug2Db1t(1,i-2)) + call matvec2(CC(1,1,i-1),Ub2(1,i-2),CUgb2(1,i-2)) + call matmat2(EUg(1,1,i-2),CC(1,1,i-1),EUgC(1,1,i-2)) + call matmat2(EUg(1,1,i-2),DD(1,1,i-1),EUgD(1,1,i-2)) + if (calc_grad) then call matvec2(Ug2der(1,1,i-2),auxvec(1),Ug2Db1tder(1,i-2)) - call matvec2(CC(1,1,iti1),Ub2(1,i-2),CUgb2(1,i-2)) - call matvec2(CC(1,1,iti1),Ub2der(1,i-2),CUgb2der(1,i-2)) - call matmat2(EUg(1,1,i-2),CC(1,1,iti1),EUgC(1,1,i-2)) - call matmat2(EUgder(1,1,i-2),CC(1,1,iti1),EUgCder(1,1,i-2)) - call matmat2(EUg(1,1,i-2),DD(1,1,iti1),EUgD(1,1,i-2)) - call matmat2(EUgder(1,1,i-2),DD(1,1,iti1),EUgDder(1,1,i-2)) -cd write (iout,*) 'i',i,' mu ',(mu(k,i-2),k=1,2), -cd & ' mu1',(b1(k,i-2),k=1,2),' mu2',(Ub2(k,i-2),k=1,2) + call matvec2(CC(1,1,i-1),Ub2der(1,i-2),CUgb2der(1,i-2)) + call matmat2(EUgder(1,1,i-2),CC(1,1,i-1),EUgCder(1,1,i-2)) + call matmat2(EUgder(1,1,i-2),DD(1,1,i-1),EUgDder(1,1,i-2)) + endif + endif enddo C Matrices dependent on two consecutive virtual-bond dihedrals. C The order of matrices is from left to right. + if (wcorr4.gt.0.0d0 .or. wcorr5.gt.0.0d0 .or.wcorr6.gt.0.0d0) + &then do i=2,nres-1 call matmat2(DtUg2(1,1,i-1),EUg(1,1,i),DtUg2EUg(1,1,i)) + if (calc_grad) then call matmat2(DtUg2der(1,1,i-1),EUg(1,1,i),DtUg2EUgder(1,1,1,i)) call matmat2(DtUg2(1,1,i-1),EUgder(1,1,i),DtUg2EUgder(1,1,2,i)) + endif call transpose2(DtUg2(1,1,i-1),auxmat(1,1)) call matmat2(auxmat(1,1),EUg(1,1,i),Ug2DtEUg(1,1,i)) + if (calc_grad) then call matmat2(auxmat(1,1),EUgder(1,1,i),Ug2DtEUgder(1,1,2,i)) call transpose2(DtUg2der(1,1,i-1),auxmat(1,1)) call matmat2(auxmat(1,1),EUg(1,1,i),Ug2DtEUgder(1,1,1,i)) + endif enddo -cd do i=1,nres -cd iti = itortyp(itype(i)) -cd write (iout,*) i -cd do j=1,2 -cd write (iout,'(2f10.5,5x,2f10.5,5x,2f10.5)') -cd & (EE(j,k,iti),k=1,2),(Ug(j,k,i),k=1,2),(EUg(j,k,i),k=1,2) -cd enddo -cd enddo + endif return end C-------------------------------------------------------------------------- @@ -1722,8 +2100,10 @@ C The potential depends both on the distance of peptide-group centers and on C the orientation of the CA-CA virtual bonds. C implicit real*8 (a-h,o-z) +#ifdef MPI + include 'mpif.h' +#endif include 'DIMENSIONS' - include 'sizesclu.dat' include 'COMMON.CONTROL' include 'COMMON.IOUNITS' include 'COMMON.GEO' @@ -1736,13 +2116,21 @@ C include 'COMMON.TORSION' include 'COMMON.VECTORS' include 'COMMON.FFIELD' + include 'COMMON.TIME1' + include 'COMMON.SPLITELE' dimension ggg(3),gggp(3),gggm(3),erij(3),dcosb(3),dcosg(3), & erder(3,3),uryg(3,3),urzg(3,3),vryg(3,3),vrzg(3,3) double precision acipa(2,2),agg(3,4),aggi(3,4),aggi1(3,4), - & aggj(3,4),aggj1(3,4),a_temp(2,2),muij(4) - common /locel/ a_temp,agg,aggi,aggi1,aggj,aggj1,j1 + & aggj(3,4),aggj1(3,4),a_temp(2,2),muij(4),gmuij(4) + common /locel/ a_temp,agg,aggi,aggi1,aggj,aggj1,a22,a23,a32,a33, + & dxi,dyi,dzi,dx_normi,dy_normi,dz_normi,xmedi,ymedi,zmedi, + & num_conti,j1,j2 c 4/26/02 - AL scaling factor for 1,4 repulsive VDW interactions +#ifdef MOMENT + double precision scal_el /1.0d0/ +#else double precision scal_el /0.5d0/ +#endif C 12/13/98 C 13-go grudnia roku pamietnego... double precision unmat(3,3) /1.0d0,0.0d0,0.0d0, @@ -1771,25 +2159,26 @@ c write (iout,*) 'i',i,' fac',fac if (wel_loc.gt.0.0d0 .or. wcorr4.gt.0.0d0 .or. wcorr5.gt.0.0d0 & .or. wcorr6.gt.0.0d0 .or. wturn3.gt.0.0d0 .or. & wturn4.gt.0.0d0 .or. wturn6.gt.0.0d0) then -cd if (wel_loc.gt.0.0d0) then - if (icheckgrad.eq.1) then - call vec_and_deriv_test - else - call vec_and_deriv - endif +c call vec_and_deriv +#ifdef TIMING + time01=MPI_Wtime() +#endif call set_matrices +#ifdef TIMING + time_mat=time_mat+MPI_Wtime()-time01 +#endif endif cd do i=1,nres-1 cd write (iout,*) 'i=',i cd do k=1,3 -cd write (iout,'(i5,2f10.5)') k,uy(k,i),uz(k,i) +cd write (iout,'(i5,2f10.5)') k,uy(k,i),uz(k,i) cd enddo cd do k=1,3 cd write (iout,'(f10.5,2x,3f10.5,2x,3f10.5)') cd & uz(k,i),(uzgrad(k,l,1,i),l=1,3),(uzgrad(k,l,2,i),l=1,3) cd enddo cd enddo - num_conti_hb=0 + t_eelecij=0.0d0 ees=0.0D0 evdw1=0.0D0 eel_loc=0.0d0 @@ -1800,14 +2189,38 @@ cd enddo num_cont_hb(i)=0 enddo cd print '(a)','Enter EELEC' -cd write (iout,*) 'iatel_s=',iatel_s,' iatel_e=',iatel_e +c write (iout,*) 'iatel_s=',iatel_s,' iatel_e=',iatel_e +c call flush(iout) do i=1,nres gel_loc_loc(i)=0.0d0 gcorr_loc(i)=0.0d0 enddo - do i=iatel_s,iatel_e - if (itype(i).eq.21 .or. itype(i+1).eq.21) cycle - if (itel(i).eq.0) goto 1215 +c +c +c 9/27/08 AL Split the interaction loop to ensure load balancing of turn terms +C +C Loop over i,i+2 and i,i+3 pairs of the peptide groups +C +C 14/01/2014 TURN3,TUNR4 does no go under periodic boundry condition + do i=iturn3_start,iturn3_end +c if (i.le.1) cycle +C write(iout,*) "tu jest i",i + if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1 +C changes suggested by Ana to avoid out of bounds +C Adam: Unnecessary: handled by iturn3_end and iturn3_start +c & .or.((i+4).gt.nres) +c & .or.((i-1).le.0) +C end of changes by Ana +C dobra zmiana wycofana + & .or. itype(i+2).eq.ntyp1 + & .or. itype(i+3).eq.ntyp1) cycle +C Adam: Instructions below will switch off existing interactions +c if(i.gt.1)then +c if(itype(i-1).eq.ntyp1)cycle +c end if +c if(i.LT.nres-3)then +c if (itype(i+4).eq.ntyp1) cycle +c end if dxi=dc(1,i) dyi=dc(2,i) dzi=dc(3,i) @@ -1817,23 +2230,225 @@ cd write (iout,*) 'iatel_s=',iatel_s,' iatel_e=',iatel_e xmedi=c(1,i)+0.5d0*dxi ymedi=c(2,i)+0.5d0*dyi zmedi=c(3,i)+0.5d0*dzi + xmedi=mod(xmedi,boxxsize) + if (xmedi.lt.0) xmedi=xmedi+boxxsize + ymedi=mod(ymedi,boxysize) + if (ymedi.lt.0) ymedi=ymedi+boxysize + zmedi=mod(zmedi,boxzsize) + if (zmedi.lt.0) zmedi=zmedi+boxzsize num_conti=0 + call eelecij(i,i+2,ees,evdw1,eel_loc) + if (wturn3.gt.0.0d0) call eturn3(i,eello_turn3) + num_cont_hb(i)=num_conti + enddo + do i=iturn4_start,iturn4_end + if (i.lt.1) cycle + if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1 +C changes suggested by Ana to avoid out of bounds +c & .or.((i+5).gt.nres) +c & .or.((i-1).le.0) +C end of changes suggested by Ana + & .or. itype(i+3).eq.ntyp1 + & .or. itype(i+4).eq.ntyp1 +c & .or. itype(i+5).eq.ntyp1 +c & .or. itype(i).eq.ntyp1 +c & .or. itype(i-1).eq.ntyp1 + & ) cycle + dxi=dc(1,i) + dyi=dc(2,i) + dzi=dc(3,i) + dx_normi=dc_norm(1,i) + dy_normi=dc_norm(2,i) + dz_normi=dc_norm(3,i) + xmedi=c(1,i)+0.5d0*dxi + ymedi=c(2,i)+0.5d0*dyi + zmedi=c(3,i)+0.5d0*dzi +C Return atom into box, boxxsize is size of box in x dimension +c 194 continue +c if (xmedi.gt.((0.5d0)*boxxsize)) xmedi=xmedi-boxxsize +c if (xmedi.lt.((-0.5d0)*boxxsize)) xmedi=xmedi+boxxsize +C Condition for being inside the proper box +c if ((xmedi.gt.((0.5d0)*boxxsize)).or. +c & (xmedi.lt.((-0.5d0)*boxxsize))) then +c go to 194 +c endif +c 195 continue +c if (ymedi.gt.((0.5d0)*boxysize)) ymedi=ymedi-boxysize +c if (ymedi.lt.((-0.5d0)*boxysize)) ymedi=ymedi+boxysize +C Condition for being inside the proper box +c if ((ymedi.gt.((0.5d0)*boxysize)).or. +c & (ymedi.lt.((-0.5d0)*boxysize))) then +c go to 195 +c endif +c 196 continue +c if (zmedi.gt.((0.5d0)*boxzsize)) zmedi=zmedi-boxzsize +c if (zmedi.lt.((-0.5d0)*boxzsize)) zmedi=zmedi+boxzsize +C Condition for being inside the proper box +c if ((zmedi.gt.((0.5d0)*boxzsize)).or. +c & (zmedi.lt.((-0.5d0)*boxzsize))) then +c go to 196 +c endif + xmedi=mod(xmedi,boxxsize) + if (xmedi.lt.0) xmedi=xmedi+boxxsize + ymedi=mod(ymedi,boxysize) + if (ymedi.lt.0) ymedi=ymedi+boxysize + zmedi=mod(zmedi,boxzsize) + if (zmedi.lt.0) zmedi=zmedi+boxzsize + + num_conti=num_cont_hb(i) +c write(iout,*) "JESTEM W PETLI" + call eelecij(i,i+3,ees,evdw1,eel_loc) + if (wturn4.gt.0.0d0 .and. itype(i+2).ne.ntyp1) + & call eturn4(i,eello_turn4) + num_cont_hb(i)=num_conti + enddo ! i +C Loop over all neighbouring boxes +C do xshift=-1,1 +C do yshift=-1,1 +C do zshift=-1,1 +c +c Loop over all pairs of interacting peptide groups except i,i+2 and i,i+3 +c +CTU KURWA + do i=iatel_s,iatel_e +C do i=75,75 +c if (i.le.1) cycle + if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1 +C changes suggested by Ana to avoid out of bounds +c & .or.((i+2).gt.nres) +c & .or.((i-1).le.0) +C end of changes by Ana +c & .or. itype(i+2).eq.ntyp1 +c & .or. itype(i-1).eq.ntyp1 + & ) cycle + dxi=dc(1,i) + dyi=dc(2,i) + dzi=dc(3,i) + dx_normi=dc_norm(1,i) + dy_normi=dc_norm(2,i) + dz_normi=dc_norm(3,i) + xmedi=c(1,i)+0.5d0*dxi + ymedi=c(2,i)+0.5d0*dyi + zmedi=c(3,i)+0.5d0*dzi + xmedi=mod(xmedi,boxxsize) + if (xmedi.lt.0) xmedi=xmedi+boxxsize + ymedi=mod(ymedi,boxysize) + if (ymedi.lt.0) ymedi=ymedi+boxysize + zmedi=mod(zmedi,boxzsize) + if (zmedi.lt.0) zmedi=zmedi+boxzsize +C xmedi=xmedi+xshift*boxxsize +C ymedi=ymedi+yshift*boxysize +C zmedi=zmedi+zshift*boxzsize + +C Return tom into box, boxxsize is size of box in x dimension +c 164 continue +c if (xmedi.gt.((xshift+0.5d0)*boxxsize)) xmedi=xmedi-boxxsize +c if (xmedi.lt.((xshift-0.5d0)*boxxsize)) xmedi=xmedi+boxxsize +C Condition for being inside the proper box +c if ((xmedi.gt.((xshift+0.5d0)*boxxsize)).or. +c & (xmedi.lt.((xshift-0.5d0)*boxxsize))) then +c go to 164 +c endif +c 165 continue +c if (ymedi.gt.((yshift+0.5d0)*boxysize)) ymedi=ymedi-boxysize +c if (ymedi.lt.((yshift-0.5d0)*boxysize)) ymedi=ymedi+boxysize +C Condition for being inside the proper box +c if ((ymedi.gt.((yshift+0.5d0)*boxysize)).or. +c & (ymedi.lt.((yshift-0.5d0)*boxysize))) then +c go to 165 +c endif +c 166 continue +c if (zmedi.gt.((zshift+0.5d0)*boxzsize)) zmedi=zmedi-boxzsize +c if (zmedi.lt.((zshift-0.5d0)*boxzsize)) zmedi=zmedi+boxzsize +cC Condition for being inside the proper box +c if ((zmedi.gt.((zshift+0.5d0)*boxzsize)).or. +c & (zmedi.lt.((zshift-0.5d0)*boxzsize))) then +c go to 166 +c endif + c write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i) + num_conti=num_cont_hb(i) +C I TU KURWA do j=ielstart(i),ielend(i) - if (itype(j).eq.21 .or. itype(j+1).eq.21) cycle - if (itel(j).eq.0) goto 1216 - ind=ind+1 +C do j=16,17 +C write (iout,*) i,j +C if (j.le.1) cycle + if (itype(j).eq.ntyp1.or. itype(j+1).eq.ntyp1 +C changes suggested by Ana to avoid out of bounds +c & .or.((j+2).gt.nres) +c & .or.((j-1).le.0) +C end of changes by Ana +c & .or.itype(j+2).eq.ntyp1 +c & .or.itype(j-1).eq.ntyp1 + &) cycle + call eelecij(i,j,ees,evdw1,eel_loc) + enddo ! j + num_cont_hb(i)=num_conti + enddo ! i +C enddo ! zshift +C enddo ! yshift +C enddo ! xshift + +c write (iout,*) "Number of loop steps in EELEC:",ind +cd do i=1,nres +cd write (iout,'(i3,3f10.5,5x,3f10.5)') +cd & i,(gel_loc(k,i),k=1,3),gel_loc_loc(i) +cd enddo +c 12/7/99 Adam eello_turn3 will be considered as a separate energy term +ccc eel_loc=eel_loc+eello_turn3 +cd print *,"Processor",fg_rank," t_eelecij",t_eelecij + return + end +C------------------------------------------------------------------------------- + subroutine eelecij(i,j,ees,evdw1,eel_loc) + implicit real*8 (a-h,o-z) + include 'DIMENSIONS' +#ifdef MPI + include "mpif.h" +#endif + include 'COMMON.CONTROL' + include 'COMMON.IOUNITS' + include 'COMMON.GEO' + include 'COMMON.VAR' + include 'COMMON.LOCAL' + include 'COMMON.CHAIN' + include 'COMMON.DERIV' + include 'COMMON.INTERACT' + include 'COMMON.CONTACTS' + include 'COMMON.TORSION' + include 'COMMON.VECTORS' + include 'COMMON.FFIELD' + include 'COMMON.TIME1' + include 'COMMON.SPLITELE' + include 'COMMON.SHIELD' + dimension ggg(3),gggp(3),gggm(3),erij(3),dcosb(3),dcosg(3), + & erder(3,3),uryg(3,3),urzg(3,3),vryg(3,3),vrzg(3,3) + double precision acipa(2,2),agg(3,4),aggi(3,4),aggi1(3,4), + & aggj(3,4),aggj1(3,4),a_temp(2,2),muij(4),gmuij1(4),gmuji1(4), + & gmuij2(4),gmuji2(4) + common /locel/ a_temp,agg,aggi,aggi1,aggj,aggj1,a22,a23,a32,a33, + & dxi,dyi,dzi,dx_normi,dy_normi,dz_normi,xmedi,ymedi,zmedi, + & num_conti,j1,j2 +c 4/26/02 - AL scaling factor for 1,4 repulsive VDW interactions +#ifdef MOMENT + double precision scal_el /1.0d0/ +#else + double precision scal_el /0.5d0/ +#endif +C 12/13/98 +C 13-go grudnia roku pamietnego... + double precision unmat(3,3) /1.0d0,0.0d0,0.0d0, + & 0.0d0,1.0d0,0.0d0, + & 0.0d0,0.0d0,1.0d0/ + integer xshift,yshift,zshift +c time00=MPI_Wtime() +cd write (iout,*) "eelecij",i,j +c ind=ind+1 iteli=itel(i) itelj=itel(j) if (j.eq.i+2 .and. itelj.eq.2) iteli=2 aaa=app(iteli,itelj) bbb=bpp(iteli,itelj) -C Diagnostics only!!! -c aaa=0.0D0 -c bbb=0.0D0 -c ael6i=0.0D0 -c ael3i=0.0D0 -C End diagnostics ael6i=ael6(iteli,itelj) ael3i=ael3(iteli,itelj) dxj=dc(1,j) @@ -1842,10 +2457,86 @@ C End diagnostics dx_normj=dc_norm(1,j) dy_normj=dc_norm(2,j) dz_normj=dc_norm(3,j) - xj=c(1,j)+0.5D0*dxj-xmedi - yj=c(2,j)+0.5D0*dyj-ymedi - zj=c(3,j)+0.5D0*dzj-zmedi +C xj=c(1,j)+0.5D0*dxj-xmedi +C yj=c(2,j)+0.5D0*dyj-ymedi +C zj=c(3,j)+0.5D0*dzj-zmedi + xj=c(1,j)+0.5D0*dxj + yj=c(2,j)+0.5D0*dyj + zj=c(3,j)+0.5D0*dzj + xj=mod(xj,boxxsize) + if (xj.lt.0) xj=xj+boxxsize + yj=mod(yj,boxysize) + if (yj.lt.0) yj=yj+boxysize + zj=mod(zj,boxzsize) + if (zj.lt.0) zj=zj+boxzsize + if ((zj.lt.0).or.(xj.lt.0).or.(yj.lt.0)) write (*,*) "CHUJ" + dist_init=(xj-xmedi)**2+(yj-ymedi)**2+(zj-zmedi)**2 + xj_safe=xj + yj_safe=yj + zj_safe=zj + isubchap=0 + do xshift=-1,1 + do yshift=-1,1 + do zshift=-1,1 + xj=xj_safe+xshift*boxxsize + yj=yj_safe+yshift*boxysize + zj=zj_safe+zshift*boxzsize + dist_temp=(xj-xmedi)**2+(yj-ymedi)**2+(zj-zmedi)**2 + if(dist_temp.lt.dist_init) then + dist_init=dist_temp + xj_temp=xj + yj_temp=yj + zj_temp=zj + isubchap=1 + endif + enddo + enddo + enddo + if (isubchap.eq.1) then + xj=xj_temp-xmedi + yj=yj_temp-ymedi + zj=zj_temp-zmedi + else + xj=xj_safe-xmedi + yj=yj_safe-ymedi + zj=zj_safe-zmedi + endif +C if ((i+3).lt.j) then !this condition keeps for turn3 and turn4 not subject to PBC +c 174 continue +c if (xj.gt.((0.5d0)*boxxsize)) xj=xj-boxxsize +c if (xj.lt.((-0.5d0)*boxxsize)) xj=xj+boxxsize +C Condition for being inside the proper box +c if ((xj.gt.((0.5d0)*boxxsize)).or. +c & (xj.lt.((-0.5d0)*boxxsize))) then +c go to 174 +c endif +c 175 continue +c if (yj.gt.((0.5d0)*boxysize)) yj=yj-boxysize +c if (yj.lt.((-0.5d0)*boxysize)) yj=yj+boxysize +C Condition for being inside the proper box +c if ((yj.gt.((0.5d0)*boxysize)).or. +c & (yj.lt.((-0.5d0)*boxysize))) then +c go to 175 +c endif +c 176 continue +c if (zj.gt.((0.5d0)*boxzsize)) zj=zj-boxzsize +c if (zj.lt.((-0.5d0)*boxzsize)) zj=zj+boxzsize +C Condition for being inside the proper box +c if ((zj.gt.((0.5d0)*boxzsize)).or. +c & (zj.lt.((-0.5d0)*boxzsize))) then +c go to 176 +c endif +C endif !endPBC condintion +C xj=xj-xmedi +C yj=yj-ymedi +C zj=zj-zmedi rij=xj*xj+yj*yj+zj*zj + + sss=sscale(sqrt(rij)) + sssgrad=sscagrad(sqrt(rij)) +c write (iout,*) "ij",i,j," rij",sqrt(rij)," r_cut",r_cut, +c & " rlamb",rlamb," sss",sss +c if (sss.gt.0.0d0) then rrmij=1.0D0/rij rij=dsqrt(rij) rmij=1.0D0/rij @@ -1861,97 +2552,233 @@ c 4/26/02 - AL scaling down 1,4 repulsive VDW interactions ev2=bbb*r6ij fac3=ael6i*r6ij fac4=ael3i*r3ij - evdwij=ev1+ev2 + evdwij=(ev1+ev2) el1=fac3*(4.0D0+fac*fac-3.0D0*(cosb*cosb+cosg*cosg)) el2=fac4*fac - eesij=el1+el2 -c write (iout,*) "i",i,iteli," j",j,itelj," eesij",eesij +C MARYSIA +C eesij=(el1+el2) C 12/26/95 - for the evaluation of multi-body H-bonding interactions ees0ij=4.0D0+fac*fac-3.0D0*(cosb*cosb+cosg*cosg) + if (shield_mode.gt.0) then +C fac_shield(i)=0.4 +C fac_shield(j)=0.6 + el1=el1*fac_shield(i)**2*fac_shield(j)**2 + el2=el2*fac_shield(i)**2*fac_shield(j)**2 + eesij=(el1+el2) + ees=ees+eesij + else + fac_shield(i)=1.0 + fac_shield(j)=1.0 + eesij=(el1+el2) ees=ees+eesij - evdw1=evdw1+evdwij + endif + evdw1=evdw1+evdwij*sss cd write(iout,'(2(2i3,2x),7(1pd12.4)/2(3(1pd12.4),5x)/)') cd & iteli,i,itelj,j,aaa,bbb,ael6i,ael3i, cd & 1.0D0/dsqrt(rrmij),evdwij,eesij, cd & xmedi,ymedi,zmedi,xj,yj,zj + + if (energy_dec) then + write (iout,'(a6,2i5,0pf7.3,2i5,3e11.3)') + &'evdw1',i,j,evdwij + &,iteli,itelj,aaa,evdw1,sss + write (iout,'(a6,2i5,0pf7.3,2f8.3)') 'ees',i,j,eesij, + &fac_shield(i),fac_shield(j) + endif + C C Calculate contributions to the Cartesian gradient. C #ifdef SPLITELE - facvdw=-6*rrmij*(ev1+evdwij) + facvdw=-6*rrmij*(ev1+evdwij)*sss facel=-3*rrmij*(el1+eesij) fac1=fac erij(1)=xj*rmij erij(2)=yj*rmij erij(3)=zj*rmij - if (calc_grad) then + * * Radial derivatives. First process both termini of the fragment (i,j) -* +* + if (calc_grad) then ggg(1)=facel*xj ggg(2)=facel*yj ggg(3)=facel*zj + if ((fac_shield(i).gt.0).and.(fac_shield(j).gt.0).and. + & (shield_mode.gt.0)) then +C print *,i,j + do ilist=1,ishield_list(i) + iresshield=shield_list(ilist,i) + do k=1,3 + rlocshield=grad_shield_side(k,ilist,i)*eesij/fac_shield(i) + & *2.0 + gshieldx(k,iresshield)=gshieldx(k,iresshield)+ + & rlocshield + & +grad_shield_loc(k,ilist,i)*eesij/fac_shield(i)*2.0 + gshieldc(k,iresshield-1)=gshieldc(k,iresshield-1)+rlocshield +C gshieldc_loc(k,iresshield)=gshieldc_loc(k,iresshield) +C & +grad_shield_loc(k,ilist,i)*eesij/fac_shield(i) +C if (iresshield.gt.i) then +C do ishi=i+1,iresshield-1 +C gshieldc(k,ishi)=gshieldc(k,ishi)+rlocshield +C & +grad_shield_loc(k,ilist,i)*eesij/fac_shield(i) +C +C enddo +C else +C do ishi=iresshield,i +C gshieldc(k,ishi)=gshieldc(k,ishi)-rlocshield +C & -grad_shield_loc(k,ilist,i)*eesij/fac_shield(i) +C +C enddo +C endif + enddo + enddo + do ilist=1,ishield_list(j) + iresshield=shield_list(ilist,j) + do k=1,3 + rlocshield=grad_shield_side(k,ilist,j)*eesij/fac_shield(j) + & *2.0 + gshieldx(k,iresshield)=gshieldx(k,iresshield)+ + & rlocshield + & +grad_shield_loc(k,ilist,j)*eesij/fac_shield(j)*2.0 + gshieldc(k,iresshield-1)=gshieldc(k,iresshield-1)+rlocshield + +C & +grad_shield_loc(k,ilist,j)*eesij/fac_shield(j) +C gshieldc_loc(k,iresshield)=gshieldc_loc(k,iresshield) +C & +grad_shield_loc(k,ilist,j)*eesij/fac_shield(j) +C if (iresshield.gt.j) then +C do ishi=j+1,iresshield-1 +C gshieldc(k,ishi)=gshieldc(k,ishi)+rlocshield +C & +grad_shield_loc(k,ilist,j)*eesij/fac_shield(j) +C +C enddo +C else +C do ishi=iresshield,j +C gshieldc(k,ishi)=gshieldc(k,ishi)-rlocshield +C & -grad_shield_loc(k,ilist,j)*eesij/fac_shield(j) +C enddo +C endif + enddo + enddo + do k=1,3 - ghalf=0.5D0*ggg(k) - gelc(k,i)=gelc(k,i)+ghalf - gelc(k,j)=gelc(k,j)+ghalf + gshieldc(k,i)=gshieldc(k,i)+ + & grad_shield(k,i)*eesij/fac_shield(i)*2.0 + gshieldc(k,j)=gshieldc(k,j)+ + & grad_shield(k,j)*eesij/fac_shield(j)*2.0 + gshieldc(k,i-1)=gshieldc(k,i-1)+ + & grad_shield(k,i)*eesij/fac_shield(i)*2.0 + gshieldc(k,j-1)=gshieldc(k,j-1)+ + & grad_shield(k,j)*eesij/fac_shield(j)*2.0 + + enddo + endif +c do k=1,3 +c ghalf=0.5D0*ggg(k) +c gelc(k,i)=gelc(k,i)+ghalf +c gelc(k,j)=gelc(k,j)+ghalf +c enddo +c 9/28/08 AL Gradient compotents will be summed only at the end +C print *,"before", gelc_long(1,i), gelc_long(1,j) + do k=1,3 + gelc_long(k,j)=gelc_long(k,j)+ggg(k) +C & +grad_shield(k,j)*eesij/fac_shield(j) + gelc_long(k,i)=gelc_long(k,i)-ggg(k) +C & +grad_shield(k,i)*eesij/fac_shield(i) +C gelc_long(k,i-1)=gelc_long(k,i-1) +C & +grad_shield(k,i)*eesij/fac_shield(i) +C gelc_long(k,j-1)=gelc_long(k,j-1) +C & +grad_shield(k,j)*eesij/fac_shield(j) enddo +C print *,"bafter", gelc_long(1,i), gelc_long(1,j) + * * Loop over residues i+1 thru j-1. * - do k=i+1,j-1 - do l=1,3 - gelc(l,k)=gelc(l,k)+ggg(l) - enddo - enddo - ggg(1)=facvdw*xj - ggg(2)=facvdw*yj - ggg(3)=facvdw*zj +cgrad do k=i+1,j-1 +cgrad do l=1,3 +cgrad gelc(l,k)=gelc(l,k)+ggg(l) +cgrad enddo +cgrad enddo + if (sss.gt.0.0) then + ggg(1)=facvdw*xj+sssgrad*rmij*evdwij*xj + ggg(2)=facvdw*yj+sssgrad*rmij*evdwij*yj + ggg(3)=facvdw*zj+sssgrad*rmij*evdwij*zj + else + ggg(1)=0.0 + ggg(2)=0.0 + ggg(3)=0.0 + endif +c do k=1,3 +c ghalf=0.5D0*ggg(k) +c gvdwpp(k,i)=gvdwpp(k,i)+ghalf +c gvdwpp(k,j)=gvdwpp(k,j)+ghalf +c enddo +c 9/28/08 AL Gradient compotents will be summed only at the end do k=1,3 - ghalf=0.5D0*ggg(k) - gvdwpp(k,i)=gvdwpp(k,i)+ghalf - gvdwpp(k,j)=gvdwpp(k,j)+ghalf + gvdwpp(k,j)=gvdwpp(k,j)+ggg(k) + gvdwpp(k,i)=gvdwpp(k,i)-ggg(k) enddo * * Loop over residues i+1 thru j-1. * - do k=i+1,j-1 - do l=1,3 - gvdwpp(l,k)=gvdwpp(l,k)+ggg(l) - enddo - enddo +cgrad do k=i+1,j-1 +cgrad do l=1,3 +cgrad gvdwpp(l,k)=gvdwpp(l,k)+ggg(l) +cgrad enddo +cgrad enddo + endif ! calc_grad #else - facvdw=ev1+evdwij - facel=el1+eesij +C MARYSIA + facvdw=(ev1+evdwij)*sss + facel=(el1+eesij) fac1=fac fac=-3*rrmij*(facvdw+facvdw+facel) erij(1)=xj*rmij erij(2)=yj*rmij erij(3)=zj*rmij - if (calc_grad) then * * Radial derivatives. First process both termini of the fragment (i,j) * + if (calc_grad) then ggg(1)=fac*xj +C+eesij*grad_shield(1,i)+eesij*grad_shield(1,j) ggg(2)=fac*yj +C+eesij*grad_shield(2,i)+eesij*grad_shield(2,j) ggg(3)=fac*zj +C+eesij*grad_shield(3,i)+eesij*grad_shield(3,j) +c do k=1,3 +c ghalf=0.5D0*ggg(k) +c gelc(k,i)=gelc(k,i)+ghalf +c gelc(k,j)=gelc(k,j)+ghalf +c enddo +c 9/28/08 AL Gradient compotents will be summed only at the end do k=1,3 - ghalf=0.5D0*ggg(k) - gelc(k,i)=gelc(k,i)+ghalf - gelc(k,j)=gelc(k,j)+ghalf + gelc_long(k,j)=gelc(k,j)+ggg(k) + gelc_long(k,i)=gelc(k,i)-ggg(k) enddo * * Loop over residues i+1 thru j-1. * - do k=i+1,j-1 - do l=1,3 - gelc(l,k)=gelc(l,k)+ggg(l) - enddo +cgrad do k=i+1,j-1 +cgrad do l=1,3 +cgrad gelc(l,k)=gelc(l,k)+ggg(l) +cgrad enddo +cgrad enddo +c 9/28/08 AL Gradient compotents will be summed only at the end + ggg(1)=facvdw*xj+sssgrad*rmij*evdwij*xj + ggg(2)=facvdw*yj+sssgrad*rmij*evdwij*yj + ggg(3)=facvdw*zj+sssgrad*rmij*evdwij*zj + do k=1,3 + gvdwpp(k,j)=gvdwpp(k,j)+ggg(k) + gvdwpp(k,i)=gvdwpp(k,i)-ggg(k) enddo + endif ! calc_grad #endif * * Angular part * + if (calc_grad) then ecosa=2.0D0*fac3*fac1+fac4 fac4=-3.0D0*fac4 fac3=-6.0D0*fac3 @@ -1964,24 +2791,41 @@ C cd print '(2i3,2(3(1pd14.5),3x))',i,j,(dcosb(k),k=1,3), cd & (dcosg(k),k=1,3) do k=1,3 - ggg(k)=ecosb*dcosb(k)+ecosg*dcosg(k) + ggg(k)=(ecosb*dcosb(k)+ecosg*dcosg(k))* + & fac_shield(i)**2*fac_shield(j)**2 enddo +c do k=1,3 +c ghalf=0.5D0*ggg(k) +c gelc(k,i)=gelc(k,i)+ghalf +c & +(ecosa*(dc_norm(k,j)-cosa*dc_norm(k,i)) +c & + ecosb*(erij(k)-cosb*dc_norm(k,i)))*vbld_inv(i+1) +c gelc(k,j)=gelc(k,j)+ghalf +c & +(ecosa*(dc_norm(k,i)-cosa*dc_norm(k,j)) +c & + ecosg*(erij(k)-cosg*dc_norm(k,j)))*vbld_inv(j+1) +c enddo +cgrad do k=i+1,j-1 +cgrad do l=1,3 +cgrad gelc(l,k)=gelc(l,k)+ggg(l) +cgrad enddo +cgrad enddo +C print *,"before22", gelc_long(1,i), gelc_long(1,j) do k=1,3 - ghalf=0.5D0*ggg(k) - gelc(k,i)=gelc(k,i)+ghalf - & +(ecosa*(dc_norm(k,j)-cosa*dc_norm(k,i)) - & + ecosb*(erij(k)-cosb*dc_norm(k,i)))*vbld_inv(i+1) - gelc(k,j)=gelc(k,j)+ghalf - & +(ecosa*(dc_norm(k,i)-cosa*dc_norm(k,j)) - & + ecosg*(erij(k)-cosg*dc_norm(k,j)))*vbld_inv(j+1) + gelc(k,i)=gelc(k,i) + & +((ecosa*(dc_norm(k,j)-cosa*dc_norm(k,i)) + & + ecosb*(erij(k)-cosb*dc_norm(k,i)))*vbld_inv(i+1)) + & *fac_shield(i)**2*fac_shield(j)**2 + gelc(k,j)=gelc(k,j) + & +((ecosa*(dc_norm(k,i)-cosa*dc_norm(k,j)) + & + ecosg*(erij(k)-cosg*dc_norm(k,j)))*vbld_inv(j+1)) + & *fac_shield(i)**2*fac_shield(j)**2 + gelc_long(k,j)=gelc_long(k,j)+ggg(k) + gelc_long(k,i)=gelc_long(k,i)-ggg(k) enddo - do k=i+1,j-1 - do l=1,3 - gelc(l,k)=gelc(l,k)+ggg(l) - enddo - enddo - endif +C print *,"before33", gelc_long(1,i), gelc_long(1,j) +C MARYSIA +c endif !sscale + endif ! calc_grad IF (wel_loc.gt.0.0d0 .or. wcorr4.gt.0.0d0 .or. wcorr5.gt.0.0d0 & .or. wcorr6.gt.0.0d0 .or. wturn3.gt.0.0d0 & .or. wturn4.gt.0.0d0 .or. wturn6.gt.0.0d0) THEN @@ -1992,6 +2836,7 @@ C Fourier series in the angles lambda1 and lambda2 (see Nishikawa et al. C Macromolecules, 1974, 7, 797-806 for definition). This correlation terms C are computed for EVERY pair of non-contiguous peptide groups. C + if (j.lt.nres-1) then j1=j+1 j2=j-1 @@ -2000,15 +2845,32 @@ C j2=j-2 endif kkk=0 + lll=0 do k=1,2 do l=1,2 kkk=kkk+1 muij(kkk)=mu(k,i)*mu(l,j) +c write(iout,*) 'mumu=', mu(k,i),mu(l,j),i,j,k,l +#ifdef NEWCORR + if (calc_grad) then + gmuij1(kkk)=gtb1(k,i+1)*mu(l,j) +c write(iout,*) 'k=',k,i,gtb1(k,i+1),gtb1(k,i+1)*mu(l,j) + gmuij2(kkk)=gUb2(k,i)*mu(l,j) + gmuji1(kkk)=mu(k,i)*gtb1(l,j+1) +c write(iout,*) 'l=',l,j,gtb1(l,j+1),gtb1(l,j+1)*mu(k,i) + gmuji2(kkk)=mu(k,i)*gUb2(l,j) + endif +#endif enddo enddo -cd write (iout,*) 'EELEC: i',i,' j',j -cd write (iout,*) 'j',j,' j1',j1,' j2',j2 -cd write(iout,*) 'muij',muij +#ifdef DEBUG + write (iout,*) 'EELEC: i',i,' j',j + write (iout,*) 'j',j,' j1',j1,' j2',j2 + write(iout,*) 'muij',muij + write (iout,*) "uy",uy(:,i) + write (iout,*) "uz",uz(:,j) + write (iout,*) "erij",erij +#endif ury=scalar(uy(1,i),erij) urz=scalar(uz(1,i),erij) vry=scalar(uy(1,j),erij) @@ -2017,15 +2879,7 @@ cd write(iout,*) 'muij',muij a23=scalar(uy(1,i),uz(1,j))-3*ury*vrz a32=scalar(uz(1,i),uy(1,j))-3*urz*vry a33=scalar(uz(1,i),uz(1,j))-3*urz*vrz -C For diagnostics only -cd a22=1.0d0 -cd a23=1.0d0 -cd a32=1.0d0 -cd a33=1.0d0 fac=dsqrt(-ael6i)*r3ij -cd write (2,*) 'fac=',fac -C For diagnostics only -cd fac=1.0d0 a22=a22*fac a23=a23*fac a32=a32*fac @@ -2033,22 +2887,17 @@ cd fac=1.0d0 cd write (iout,'(4i5,4f10.5)') cd & i,itortyp(itype(i)),j,itortyp(itype(j)),a22,a23,a32,a33 cd write (iout,'(6f10.5)') (muij(k),k=1,4),fac,eel_loc_ij -cd write (iout,'(2(3f10.5,5x)/2(3f10.5,5x))') (uy(k,i),k=1,3), -cd & (uz(k,i),k=1,3),(uy(k,j),k=1,3),(uz(k,j),k=1,3) +cd write (iout,'(2(3f10.5,5x)/2(3f10.5,5x))') uy(:,i),uz(:,i), +cd & uy(:,j),uz(:,j) cd write (iout,'(4f10.5)') cd & scalar(uy(1,i),uy(1,j)),scalar(uy(1,i),uz(1,j)), cd & scalar(uz(1,i),uy(1,j)),scalar(uz(1,i),uz(1,j)) cd write (iout,'(4f10.5)') ury,urz,vry,vrz -cd write (iout,'(2i3,9f10.5/)') i,j, +cd write (iout,'(9f10.5/)') cd & fac22,a22,fac23,a23,fac32,a32,fac33,a33,eel_loc_ij - if (calc_grad) then C Derivatives of the elements of A in virtual-bond vectors + if (calc_grad) then call unormderiv(erij(1),unmat(1,1),rmij,erder(1,1)) -cd do k=1,3 -cd do l=1,3 -cd erder(k,l)=0.0d0 -cd enddo -cd enddo do k=1,3 uryg(k,1)=scalar(erder(1,k),uy(1,i)) uryg(k,2)=scalar(uygrad(1,k,1,i),erij(1)) @@ -2063,24 +2912,12 @@ cd enddo vrzg(k,2)=scalar(uzgrad(1,k,1,j),erij(1)) vrzg(k,3)=scalar(uzgrad(1,k,2,j),erij(1)) enddo -cd do k=1,3 -cd do l=1,3 -cd uryg(k,l)=0.0d0 -cd urzg(k,l)=0.0d0 -cd vryg(k,l)=0.0d0 -cd vrzg(k,l)=0.0d0 -cd enddo -cd enddo C Compute radial contributions to the gradient facr=-3.0d0*rrmij a22der=a22*facr a23der=a23*facr a32der=a32*facr a33der=a33*facr -cd a22der=0.0d0 -cd a23der=0.0d0 -cd a32der=0.0d0 -cd a33der=0.0d0 agg(1,1)=a22der*xj agg(2,1)=a22der*yj agg(3,1)=a22der*zj @@ -2103,36 +2940,36 @@ C Add the contributions coming from er enddo do k=1,3 C Derivatives in DC(i) - ghalf1=0.5d0*agg(k,1) - ghalf2=0.5d0*agg(k,2) - ghalf3=0.5d0*agg(k,3) - ghalf4=0.5d0*agg(k,4) +cgrad ghalf1=0.5d0*agg(k,1) +cgrad ghalf2=0.5d0*agg(k,2) +cgrad ghalf3=0.5d0*agg(k,3) +cgrad ghalf4=0.5d0*agg(k,4) aggi(k,1)=fac*(scalar(uygrad(1,k,1,i),uy(1,j)) - & -3.0d0*uryg(k,2)*vry)+ghalf1 + & -3.0d0*uryg(k,2)*vry)!+ghalf1 aggi(k,2)=fac*(scalar(uygrad(1,k,1,i),uz(1,j)) - & -3.0d0*uryg(k,2)*vrz)+ghalf2 + & -3.0d0*uryg(k,2)*vrz)!+ghalf2 aggi(k,3)=fac*(scalar(uzgrad(1,k,1,i),uy(1,j)) - & -3.0d0*urzg(k,2)*vry)+ghalf3 + & -3.0d0*urzg(k,2)*vry)!+ghalf3 aggi(k,4)=fac*(scalar(uzgrad(1,k,1,i),uz(1,j)) - & -3.0d0*urzg(k,2)*vrz)+ghalf4 + & -3.0d0*urzg(k,2)*vrz)!+ghalf4 C Derivatives in DC(i+1) aggi1(k,1)=fac*(scalar(uygrad(1,k,2,i),uy(1,j)) - & -3.0d0*uryg(k,3)*vry)+agg(k,1) + & -3.0d0*uryg(k,3)*vry)!+agg(k,1) aggi1(k,2)=fac*(scalar(uygrad(1,k,2,i),uz(1,j)) - & -3.0d0*uryg(k,3)*vrz)+agg(k,2) + & -3.0d0*uryg(k,3)*vrz)!+agg(k,2) aggi1(k,3)=fac*(scalar(uzgrad(1,k,2,i),uy(1,j)) - & -3.0d0*urzg(k,3)*vry)+agg(k,3) + & -3.0d0*urzg(k,3)*vry)!+agg(k,3) aggi1(k,4)=fac*(scalar(uzgrad(1,k,2,i),uz(1,j)) - & -3.0d0*urzg(k,3)*vrz)+agg(k,4) + & -3.0d0*urzg(k,3)*vrz)!+agg(k,4) C Derivatives in DC(j) aggj(k,1)=fac*(scalar(uygrad(1,k,1,j),uy(1,i)) - & -3.0d0*vryg(k,2)*ury)+ghalf1 + & -3.0d0*vryg(k,2)*ury)!+ghalf1 aggj(k,2)=fac*(scalar(uzgrad(1,k,1,j),uy(1,i)) - & -3.0d0*vrzg(k,2)*ury)+ghalf2 + & -3.0d0*vrzg(k,2)*ury)!+ghalf2 aggj(k,3)=fac*(scalar(uygrad(1,k,1,j),uz(1,i)) - & -3.0d0*vryg(k,2)*urz)+ghalf3 + & -3.0d0*vryg(k,2)*urz)!+ghalf3 aggj(k,4)=fac*(scalar(uzgrad(1,k,1,j),uz(1,i)) - & -3.0d0*vrzg(k,2)*urz)+ghalf4 + & -3.0d0*vrzg(k,2)*urz)!+ghalf4 C Derivatives in DC(j+1) or DC(nres-1) aggj1(k,1)=fac*(scalar(uygrad(1,k,2,j),uy(1,i)) & -3.0d0*vryg(k,3)*ury) @@ -2142,41 +2979,20 @@ C Derivatives in DC(j+1) or DC(nres-1) & -3.0d0*vryg(k,3)*urz) aggj1(k,4)=fac*(scalar(uzgrad(1,k,2,j),uz(1,i)) & -3.0d0*vrzg(k,3)*urz) -cd aggi(k,1)=ghalf1 -cd aggi(k,2)=ghalf2 -cd aggi(k,3)=ghalf3 -cd aggi(k,4)=ghalf4 -C Derivatives in DC(i+1) -cd aggi1(k,1)=agg(k,1) -cd aggi1(k,2)=agg(k,2) -cd aggi1(k,3)=agg(k,3) -cd aggi1(k,4)=agg(k,4) -C Derivatives in DC(j) -cd aggj(k,1)=ghalf1 -cd aggj(k,2)=ghalf2 -cd aggj(k,3)=ghalf3 -cd aggj(k,4)=ghalf4 -C Derivatives in DC(j+1) -cd aggj1(k,1)=0.0d0 -cd aggj1(k,2)=0.0d0 -cd aggj1(k,3)=0.0d0 -cd aggj1(k,4)=0.0d0 - if (j.eq.nres-1 .and. i.lt.j-2) then - do l=1,4 - aggj1(k,l)=aggj1(k,l)+agg(k,l) -cd aggj1(k,l)=agg(k,l) - enddo - endif +cgrad if (j.eq.nres-1 .and. i.lt.j-2) then +cgrad do l=1,4 +cgrad aggj1(k,l)=aggj1(k,l)+agg(k,l) +cgrad enddo +cgrad endif enddo - endif -c goto 11111 -C Check the loc-el terms by numerical integration + endif ! calc_grad acipa(1,1)=a22 acipa(1,2)=a23 acipa(2,1)=a32 acipa(2,2)=a33 a22=-a22 a23=-a23 + if (calc_grad) then do l=1,2 do k=1,3 agg(k,l)=-agg(k,l) @@ -2186,6 +3002,7 @@ C Check the loc-el terms by numerical integration aggj1(k,l)=-aggj1(k,l) enddo enddo + endif ! calc_grad if (j.lt.nres-1) then a22=-a22 a32=-a32 @@ -2214,63 +3031,188 @@ C Check the loc-el terms by numerical integration enddo endif ENDIF ! WCORR -11111 continue IF (wel_loc.gt.0.0d0) THEN C Contribution to the local-electrostatic energy coming from the i-j pair eel_loc_ij=a22*muij(1)+a23*muij(2)+a32*muij(3) & +a33*muij(4) -cd write (iout,*) 'i',i,' j',j,' eel_loc_ij',eel_loc_ij -cd write (iout,*) a22,muij(1),a23,muij(2),a32,muij(3) +#ifdef DEBUG + write (iout,*) "muij",muij," a22",a22," a23",a23," a32",a32, + & " a33",a33 + write (iout,*) "ij",i,j," eel_loc_ij",eel_loc_ij, + & " wel_loc",wel_loc +#endif + if (shield_mode.eq.0) then + fac_shield(i)=1.0 + fac_shield(j)=1.0 +C else +C fac_shield(i)=0.4 +C fac_shield(j)=0.6 + endif + eel_loc_ij=eel_loc_ij + & *fac_shield(i)*fac_shield(j) + if (energy_dec) write (iout,'(a6,2i5,0pf7.3)') + & 'eelloc',i,j,eel_loc_ij +c if (eel_loc_ij.ne.0) +c & write (iout,'(a4,2i4,8f9.5)')'chuj', +c & i,j,a22,muij(1),a23,muij(2),a32,muij(3),a33,muij(4) + eel_loc=eel_loc+eel_loc_ij -C Partial derivatives in virtual-bond dihedral angles gamma +C Now derivative over eel_loc if (calc_grad) then + if ((fac_shield(i).gt.0).and.(fac_shield(j).gt.0).and. + & (shield_mode.gt.0)) then +C print *,i,j + + do ilist=1,ishield_list(i) + iresshield=shield_list(ilist,i) + do k=1,3 + rlocshield=grad_shield_side(k,ilist,i)*eel_loc_ij + & /fac_shield(i) +C & *2.0 + gshieldx_ll(k,iresshield)=gshieldx_ll(k,iresshield)+ + & rlocshield + & +grad_shield_loc(k,ilist,i)*eel_loc_ij/fac_shield(i) + gshieldc_ll(k,iresshield-1)=gshieldc_ll(k,iresshield-1) + & +rlocshield + enddo + enddo + do ilist=1,ishield_list(j) + iresshield=shield_list(ilist,j) + do k=1,3 + rlocshield=grad_shield_side(k,ilist,j)*eel_loc_ij + & /fac_shield(j) +C & *2.0 + gshieldx_ll(k,iresshield)=gshieldx_ll(k,iresshield)+ + & rlocshield + & +grad_shield_loc(k,ilist,j)*eel_loc_ij/fac_shield(j) + gshieldc_ll(k,iresshield-1)=gshieldc_ll(k,iresshield-1) + & +rlocshield + + enddo + enddo + + do k=1,3 + gshieldc_ll(k,i)=gshieldc_ll(k,i)+ + & grad_shield(k,i)*eel_loc_ij/fac_shield(i) + gshieldc_ll(k,j)=gshieldc_ll(k,j)+ + & grad_shield(k,j)*eel_loc_ij/fac_shield(j) + gshieldc_ll(k,i-1)=gshieldc_ll(k,i-1)+ + & grad_shield(k,i)*eel_loc_ij/fac_shield(i) + gshieldc_ll(k,j-1)=gshieldc_ll(k,j-1)+ + & grad_shield(k,j)*eel_loc_ij/fac_shield(j) + enddo + endif + + +c write (iout,*) 'i',i,' j',j,itype(i),itype(j), +c & ' eel_loc_ij',eel_loc_ij +C write(iout,*) 'muije=',i,j,muij(1),muij(2),muij(3),muij(4) +C Calculate patrial derivative for theta angle +#ifdef NEWCORR + geel_loc_ij=(a22*gmuij1(1) + & +a23*gmuij1(2) + & +a32*gmuij1(3) + & +a33*gmuij1(4)) + & *fac_shield(i)*fac_shield(j) +c write(iout,*) "derivative over thatai" +c write(iout,*) a22*gmuij1(1), a23*gmuij1(2) ,a32*gmuij1(3), +c & a33*gmuij1(4) + gloc(nphi+i,icg)=gloc(nphi+i,icg)+ + & geel_loc_ij*wel_loc +c write(iout,*) "derivative over thatai-1" +c write(iout,*) a22*gmuij2(1), a23*gmuij2(2) ,a32*gmuij2(3), +c & a33*gmuij2(4) + geel_loc_ij= + & a22*gmuij2(1) + & +a23*gmuij2(2) + & +a32*gmuij2(3) + & +a33*gmuij2(4) + gloc(nphi+i-1,icg)=gloc(nphi+i-1,icg)+ + & geel_loc_ij*wel_loc + & *fac_shield(i)*fac_shield(j) + +c Derivative over j residue + geel_loc_ji=a22*gmuji1(1) + & +a23*gmuji1(2) + & +a32*gmuji1(3) + & +a33*gmuji1(4) +c write(iout,*) "derivative over thataj" +c write(iout,*) a22*gmuji1(1), a23*gmuji1(2) ,a32*gmuji1(3), +c & a33*gmuji1(4) + + gloc(nphi+j,icg)=gloc(nphi+j,icg)+ + & geel_loc_ji*wel_loc + & *fac_shield(i)*fac_shield(j) + + geel_loc_ji= + & +a22*gmuji2(1) + & +a23*gmuji2(2) + & +a32*gmuji2(3) + & +a33*gmuji2(4) +c write(iout,*) "derivative over thataj-1" +c write(iout,*) a22*gmuji2(1), a23*gmuji2(2) ,a32*gmuji2(3), +c & a33*gmuji2(4) + gloc(nphi+j-1,icg)=gloc(nphi+j-1,icg)+ + & geel_loc_ji*wel_loc + & *fac_shield(i)*fac_shield(j) +#endif +cd write (iout,*) 'i',i,' j',j,' eel_loc_ij',eel_loc_ij + +C Partial derivatives in virtual-bond dihedral angles gamma if (i.gt.1) & gel_loc_loc(i-1)=gel_loc_loc(i-1)+ - & a22*muder(1,i)*mu(1,j)+a23*muder(1,i)*mu(2,j) - & +a32*muder(2,i)*mu(1,j)+a33*muder(2,i)*mu(2,j) - gel_loc_loc(j-1)=gel_loc_loc(j-1)+ - & a22*mu(1,i)*muder(1,j)+a23*mu(1,i)*muder(2,j) - & +a32*mu(2,i)*muder(1,j)+a33*mu(2,i)*muder(2,j) -cd call checkint3(i,j,mu1,mu2,a22,a23,a32,a33,acipa,eel_loc_ij) -cd write(iout,*) 'agg ',agg -cd write(iout,*) 'aggi ',aggi -cd write(iout,*) 'aggi1',aggi1 -cd write(iout,*) 'aggj ',aggj -cd write(iout,*) 'aggj1',aggj1 + & (a22*muder(1,i)*mu(1,j)+a23*muder(1,i)*mu(2,j) + & +a32*muder(2,i)*mu(1,j)+a33*muder(2,i)*mu(2,j)) + & *fac_shield(i)*fac_shield(j) + gel_loc_loc(j-1)=gel_loc_loc(j-1)+ + & (a22*mu(1,i)*muder(1,j)+a23*mu(1,i)*muder(2,j) + & +a32*mu(2,i)*muder(1,j)+a33*mu(2,i)*muder(2,j)) + & *fac_shield(i)*fac_shield(j) C Derivatives of eello in DC(i+1) thru DC(j-1) or DC(nres-2) do l=1,3 - ggg(l)=agg(l,1)*muij(1)+ - & agg(l,2)*muij(2)+agg(l,3)*muij(3)+agg(l,4)*muij(4) - enddo - do k=i+2,j2 - do l=1,3 - gel_loc(l,k)=gel_loc(l,k)+ggg(l) - enddo + ggg(l)=(agg(l,1)*muij(1)+ + & agg(l,2)*muij(2)+agg(l,3)*muij(3)+agg(l,4)*muij(4)) + & *fac_shield(i)*fac_shield(j) + gel_loc_long(l,j)=gel_loc_long(l,j)+ggg(l) + gel_loc_long(l,i)=gel_loc_long(l,i)-ggg(l) +cgrad ghalf=0.5d0*ggg(l) +cgrad gel_loc(l,i)=gel_loc(l,i)+ghalf +cgrad gel_loc(l,j)=gel_loc(l,j)+ghalf enddo +cgrad do k=i+1,j2 +cgrad do l=1,3 +cgrad gel_loc(l,k)=gel_loc(l,k)+ggg(l) +cgrad enddo +cgrad enddo C Remaining derivatives of eello do l=1,3 - gel_loc(l,i)=gel_loc(l,i)+aggi(l,1)*muij(1)+ - & aggi(l,2)*muij(2)+aggi(l,3)*muij(3)+aggi(l,4)*muij(4) - gel_loc(l,i+1)=gel_loc(l,i+1)+aggi1(l,1)*muij(1)+ - & aggi1(l,2)*muij(2)+aggi1(l,3)*muij(3)+aggi1(l,4)*muij(4) - gel_loc(l,j)=gel_loc(l,j)+aggj(l,1)*muij(1)+ - & aggj(l,2)*muij(2)+aggj(l,3)*muij(3)+aggj(l,4)*muij(4) - gel_loc(l,j1)=gel_loc(l,j1)+aggj1(l,1)*muij(1)+ - & aggj1(l,2)*muij(2)+aggj1(l,3)*muij(3)+aggj1(l,4)*muij(4) + gel_loc(l,i)=gel_loc(l,i)+(aggi(l,1)*muij(1)+ + & aggi(l,2)*muij(2)+aggi(l,3)*muij(3)+aggi(l,4)*muij(4)) + & *fac_shield(i)*fac_shield(j) + + gel_loc(l,i+1)=gel_loc(l,i+1)+(aggi1(l,1)*muij(1)+ + & aggi1(l,2)*muij(2)+aggi1(l,3)*muij(3)+aggi1(l,4)*muij(4)) + & *fac_shield(i)*fac_shield(j) + + gel_loc(l,j)=gel_loc(l,j)+(aggj(l,1)*muij(1)+ + & aggj(l,2)*muij(2)+aggj(l,3)*muij(3)+aggj(l,4)*muij(4)) + & *fac_shield(i)*fac_shield(j) + + gel_loc(l,j1)=gel_loc(l,j1)+(aggj1(l,1)*muij(1)+ + & aggj1(l,2)*muij(2)+aggj1(l,3)*muij(3)+aggj1(l,4)*muij(4)) + & *fac_shield(i)*fac_shield(j) + enddo - endif + endif ! calc_grad ENDIF - if (wturn3.gt.0.0d0 .or. wturn4.gt.0.0d0) then -C Contributions from turns - a_temp(1,1)=a22 - a_temp(1,2)=a23 - a_temp(2,1)=a32 - a_temp(2,2)=a33 - call eturn34(i,j,eello_turn3,eello_turn4) - endif + + C Change 12/26/95 to calculate four-body contributions to H-bonding energy - if (j.gt.i+1 .and. num_conti.le.maxconts) then +c if (j.gt.i+1 .and. num_conti.le.maxconts) then + if (wcorr+wcorr4+wcorr5+wcorr6.gt.0.0d0 + & .and. num_conti.le.maxconts) then +c write (iout,*) i,j," entered corr" C C Calculate the contact function. The ith column of the array JCONT will C contain the numbers of atoms that make contacts with the atom I (of numbers @@ -2288,6 +3230,8 @@ c r0ij=1.55D0*rpp(iteli,itelj) & ' will skip next contacts for this conf.' else jcont_hb(num_conti,i)=j +cd write (iout,*) "i",i," j",j," num_conti",num_conti, +cd & " jcont_hb",jcont_hb(num_conti,i) IF (wcorr4.gt.0.0d0 .or. wcorr5.gt.0.0d0 .or. & wcorr6.gt.0.0d0 .or. wturn6.gt.0.0d0) THEN C 9/30/99 (AL) - store components necessary to evaluate higher-order loc-el @@ -2300,42 +3244,10 @@ C --- Electrostatic-interaction matrix --- a_chuj(2,1,num_conti,i)=a32 a_chuj(2,2,num_conti,i)=a33 C --- Gradient of rij + if (calc_grad) then do kkk=1,3 grij_hb_cont(kkk,num_conti,i)=erij(kkk) enddo -c if (i.eq.1) then -c a_chuj(1,1,num_conti,i)=-0.61d0 -c a_chuj(1,2,num_conti,i)= 0.4d0 -c a_chuj(2,1,num_conti,i)= 0.65d0 -c a_chuj(2,2,num_conti,i)= 0.50d0 -c else if (i.eq.2) then -c a_chuj(1,1,num_conti,i)= 0.0d0 -c a_chuj(1,2,num_conti,i)= 0.0d0 -c a_chuj(2,1,num_conti,i)= 0.0d0 -c a_chuj(2,2,num_conti,i)= 0.0d0 -c endif -C --- and its gradients -cd write (iout,*) 'i',i,' j',j -cd do kkk=1,3 -cd write (iout,*) 'iii 1 kkk',kkk -cd write (iout,*) agg(kkk,:) -cd enddo -cd do kkk=1,3 -cd write (iout,*) 'iii 2 kkk',kkk -cd write (iout,*) aggi(kkk,:) -cd enddo -cd do kkk=1,3 -cd write (iout,*) 'iii 3 kkk',kkk -cd write (iout,*) aggi1(kkk,:) -cd enddo -cd do kkk=1,3 -cd write (iout,*) 'iii 4 kkk',kkk -cd write (iout,*) aggj(kkk,:) -cd enddo -cd do kkk=1,3 -cd write (iout,*) 'iii 5 kkk',kkk -cd write (iout,*) aggj1(kkk,:) -cd enddo kkll=0 do k=1,2 do l=1,2 @@ -2346,12 +3258,10 @@ cd enddo a_chuj_der(k,l,m,3,num_conti,i)=aggi1(m,kkll) a_chuj_der(k,l,m,4,num_conti,i)=aggj(m,kkll) a_chuj_der(k,l,m,5,num_conti,i)=aggj1(m,kkll) -c do mm=1,5 -c a_chuj_der(k,l,m,mm,num_conti,i)=0.0d0 -c enddo enddo enddo enddo + endif ! calc_grad ENDIF IF (wcorr4.eq.0.0d0 .and. wcorr.gt.0.0d0) THEN C Calculate contact energies @@ -2361,21 +3271,42 @@ C Calculate contact energies cosbg2=cosb-cosg c fac3=dsqrt(-ael6i)/r0ij**3 fac3=dsqrt(-ael6i)*r3ij - ees0pij=dsqrt(4.0D0+cosa4+wij*wij-3.0D0*cosbg1*cosbg1) - ees0mij=dsqrt(4.0D0-cosa4+wij*wij-3.0D0*cosbg2*cosbg2) +c ees0pij=dsqrt(4.0D0+cosa4+wij*wij-3.0D0*cosbg1*cosbg1) + ees0tmp=4.0D0+cosa4+wij*wij-3.0D0*cosbg1*cosbg1 + if (ees0tmp.gt.0) then + ees0pij=dsqrt(ees0tmp) + else + ees0pij=0 + endif +c ees0mij=dsqrt(4.0D0-cosa4+wij*wij-3.0D0*cosbg2*cosbg2) + ees0tmp=4.0D0-cosa4+wij*wij-3.0D0*cosbg2*cosbg2 + if (ees0tmp.gt.0) then + ees0mij=dsqrt(ees0tmp) + else + ees0mij=0 + endif c ees0mij=0.0D0 + if (shield_mode.eq.0) then + fac_shield(i)=1.0d0 + fac_shield(j)=1.0d0 + else + ees0plist(num_conti,i)=j +C fac_shield(i)=0.4d0 +C fac_shield(j)=0.6d0 + endif ees0p(num_conti,i)=0.5D0*fac3*(ees0pij+ees0mij) + & *fac_shield(i)*fac_shield(j) ees0m(num_conti,i)=0.5D0*fac3*(ees0pij-ees0mij) + & *fac_shield(i)*fac_shield(j) C Diagnostics. Comment out or remove after debugging! c ees0p(num_conti,i)=0.5D0*fac3*ees0pij c ees0m(num_conti,i)=0.5D0*fac3*ees0mij c ees0m(num_conti,i)=0.0D0 C End diagnostics. -c write (iout,*) 'i=',i,' j=',j,' rij=',rij,' r0ij=',r0ij, -c & ' ees0ij=',ees0p(num_conti,i),ees0m(num_conti,i),' fcont=',fcont - facont_hb(num_conti,i)=fcont - if (calc_grad) then +c write (iout,*) 'i=',i,' j=',j,' rij=',rij,' r0ij=',r0ij, +c & ' ees0ij=',ees0p(num_conti,i),ees0m(num_conti,i),' fcont=',fcont C Angular derivatives of the contact function + ees0pij1=fac3/ees0pij ees0mij1=fac3/ees0mij fac3p=-3.0D0*fac3*rrmij @@ -2402,6 +3333,9 @@ c ecosam=0.0D0 c ecosbm=0.0D0 c ecosgm=0.0D0 C End diagnostics + facont_hb(num_conti,i)=fcont + + if (calc_grad) then fprimcont=fprimcont/rij cd facont_hb(num_conti,i)=1.0D0 C Following line is for diagnostics. @@ -2425,24 +3359,39 @@ C Derivatives due to the contact function gacont_hbr(2,num_conti,i)=fprimcont*yj gacont_hbr(3,num_conti,i)=fprimcont*zj do k=1,3 - ghalfp=0.5D0*gggp(k) - ghalfm=0.5D0*gggm(k) - gacontp_hb1(k,num_conti,i)=ghalfp +c +c 10/24/08 cgrad and ! comments indicate the parts of the code removed +c following the change of gradient-summation algorithm. +c +cgrad ghalfp=0.5D0*gggp(k) +cgrad ghalfm=0.5D0*gggm(k) + gacontp_hb1(k,num_conti,i)=!ghalfp & +(ecosap*(dc_norm(k,j)-cosa*dc_norm(k,i)) & + ecosbp*(erij(k)-cosb*dc_norm(k,i)))*vbld_inv(i+1) - gacontp_hb2(k,num_conti,i)=ghalfp + & *fac_shield(i)*fac_shield(j) + + gacontp_hb2(k,num_conti,i)=!ghalfp & +(ecosap*(dc_norm(k,i)-cosa*dc_norm(k,j)) & + ecosgp*(erij(k)-cosg*dc_norm(k,j)))*vbld_inv(j+1) + & *fac_shield(i)*fac_shield(j) + gacontp_hb3(k,num_conti,i)=gggp(k) - gacontm_hb1(k,num_conti,i)=ghalfm + & *fac_shield(i)*fac_shield(j) + + gacontm_hb1(k,num_conti,i)=!ghalfm & +(ecosam*(dc_norm(k,j)-cosa*dc_norm(k,i)) & + ecosbm*(erij(k)-cosb*dc_norm(k,i)))*vbld_inv(i+1) - gacontm_hb2(k,num_conti,i)=ghalfm + & *fac_shield(i)*fac_shield(j) + + gacontm_hb2(k,num_conti,i)=!ghalfm & +(ecosam*(dc_norm(k,i)-cosa*dc_norm(k,j)) & + ecosgm*(erij(k)-cosg*dc_norm(k,j)))*vbld_inv(j+1) + & *fac_shield(i)*fac_shield(j) + gacontm_hb3(k,num_conti,i)=gggm(k) + & *fac_shield(i)*fac_shield(j) + enddo - endif C Diagnostics. Comment out or remove after debugging! cdiag do k=1,3 cdiag gacontp_hb1(k,num_conti,i)=0.0D0 @@ -2452,29 +3401,40 @@ cdiag gacontm_hb1(k,num_conti,i)=0.0D0 cdiag gacontm_hb2(k,num_conti,i)=0.0D0 cdiag gacontm_hb3(k,num_conti,i)=0.0D0 cdiag enddo + + endif ! calc_grad + ENDIF ! wcorr endif ! num_conti.le.maxconts endif ! fcont.gt.0 endif ! j.gt.i+1 - 1216 continue - enddo ! j - num_cont_hb(i)=num_conti - 1215 continue - enddo ! i -cd do i=1,nres -cd write (iout,'(i3,3f10.5,5x,3f10.5)') -cd & i,(gel_loc(k,i),k=1,3),gel_loc_loc(i) -cd enddo -c 12/7/99 Adam eello_turn3 will be considered as a separate energy term -ccc eel_loc=eel_loc+eello_turn3 + if (calc_grad) then + if (wturn3.gt.0.0d0 .or. wturn4.gt.0.0d0) then + do k=1,4 + do l=1,3 + ghalf=0.5d0*agg(l,k) + aggi(l,k)=aggi(l,k)+ghalf + aggi1(l,k)=aggi1(l,k)+agg(l,k) + aggj(l,k)=aggj(l,k)+ghalf + enddo + enddo + if (j.eq.nres-1 .and. i.lt.j-2) then + do k=1,4 + do l=1,3 + aggj1(l,k)=aggj1(l,k)+agg(l,k) + enddo + enddo + endif + endif + endif ! calc_grad +c t_eelecij=t_eelecij+MPI_Wtime()-time00 return end C----------------------------------------------------------------------------- - subroutine eturn34(i,j,eello_turn3,eello_turn4) + subroutine eturn3(i,eello_turn3) C Third- and fourth-order contributions from turns implicit real*8 (a-h,o-z) include 'DIMENSIONS' - include 'sizesclu.dat' include 'COMMON.IOUNITS' include 'COMMON.GEO' include 'COMMON.VAR' @@ -2486,14 +3446,25 @@ C Third- and fourth-order contributions from turns include 'COMMON.TORSION' include 'COMMON.VECTORS' include 'COMMON.FFIELD' + include 'COMMON.CONTROL' + include 'COMMON.SHIELD' dimension ggg(3) double precision auxmat(2,2),auxmat1(2,2),auxmat2(2,2),pizda(2,2), & e1t(2,2),e2t(2,2),e3t(2,2),e1tder(2,2),e2tder(2,2),e3tder(2,2), - & e1a(2,2),ae3(2,2),ae3e2(2,2),auxvec(2),auxvec1(2) + & e1a(2,2),ae3(2,2),ae3e2(2,2),auxvec(2),auxvec1(2),gpizda1(2,2), + & gpizda2(2,2),auxgmat1(2,2),auxgmatt1(2,2), + & auxgmat2(2,2),auxgmatt2(2,2) double precision agg(3,4),aggi(3,4),aggi1(3,4), - & aggj(3,4),aggj1(3,4),a_temp(2,2) - common /locel/ a_temp,agg,aggi,aggi1,aggj,aggj1,j1,j2 - if (j.eq.i+2) then + & aggj(3,4),aggj1(3,4),a_temp(2,2),auxmat3(2,2) + common /locel/ a_temp,agg,aggi,aggi1,aggj,aggj1,a22,a23,a32,a33, + & dxi,dyi,dzi,dx_normi,dy_normi,dz_normi,xmedi,ymedi,zmedi, + & num_conti,j1,j2 + j=i+2 +c write (iout,*) "eturn3",i,j,j1,j2 + a_temp(1,1)=a22 + a_temp(1,2)=a23 + a_temp(2,1)=a32 + a_temp(2,2)=a33 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC C C Third-order contributions @@ -2506,47 +3477,132 @@ C CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC cd call checkint_turn3(i,a_temp,eello_turn3_num) call matmat2(EUg(1,1,i+1),EUg(1,1,i+2),auxmat(1,1)) +c auxalary matices for theta gradient +c auxalary matrix for i+1 and constant i+2 + call matmat2(gtEUg(1,1,i+1),EUg(1,1,i+2),auxgmat1(1,1)) +c auxalary matrix for i+2 and constant i+1 + call matmat2(EUg(1,1,i+1),gtEUg(1,1,i+2),auxgmat2(1,1)) call transpose2(auxmat(1,1),auxmat1(1,1)) + call transpose2(auxgmat1(1,1),auxgmatt1(1,1)) + call transpose2(auxgmat2(1,1),auxgmatt2(1,1)) call matmat2(a_temp(1,1),auxmat1(1,1),pizda(1,1)) + call matmat2(a_temp(1,1),auxgmatt1(1,1),gpizda1(1,1)) + call matmat2(a_temp(1,1),auxgmatt2(1,1),gpizda2(1,1)) + if (shield_mode.eq.0) then + fac_shield(i)=1.0 + fac_shield(j)=1.0 +C else +C fac_shield(i)=0.4 +C fac_shield(j)=0.6 + endif eello_turn3=eello_turn3+0.5d0*(pizda(1,1)+pizda(2,2)) + & *fac_shield(i)*fac_shield(j) + eello_t3=0.5d0*(pizda(1,1)+pizda(2,2)) + & *fac_shield(i)*fac_shield(j) + if (energy_dec) write (iout,'(6heturn3,2i5,0pf7.3)') i,i+2, + & eello_t3 + if (calc_grad) then +C#ifdef NEWCORR +C Derivatives in theta + gloc(nphi+i,icg)=gloc(nphi+i,icg) + & +0.5d0*(gpizda1(1,1)+gpizda1(2,2))*wturn3 + & *fac_shield(i)*fac_shield(j) + gloc(nphi+i+1,icg)=gloc(nphi+i+1,icg) + & +0.5d0*(gpizda2(1,1)+gpizda2(2,2))*wturn3 + & *fac_shield(i)*fac_shield(j) +C#endif + +C Derivatives in shield mode + if ((fac_shield(i).gt.0).and.(fac_shield(j).gt.0).and. + & (shield_mode.gt.0)) then +C print *,i,j + + do ilist=1,ishield_list(i) + iresshield=shield_list(ilist,i) + do k=1,3 + rlocshield=grad_shield_side(k,ilist,i)*eello_t3/fac_shield(i) +C & *2.0 + gshieldx_t3(k,iresshield)=gshieldx_t3(k,iresshield)+ + & rlocshield + & +grad_shield_loc(k,ilist,i)*eello_t3/fac_shield(i) + gshieldc_t3(k,iresshield-1)=gshieldc_t3(k,iresshield-1) + & +rlocshield + enddo + enddo + do ilist=1,ishield_list(j) + iresshield=shield_list(ilist,j) + do k=1,3 + rlocshield=grad_shield_side(k,ilist,j)*eello_t3/fac_shield(j) +C & *2.0 + gshieldx_t3(k,iresshield)=gshieldx_t3(k,iresshield)+ + & rlocshield + & +grad_shield_loc(k,ilist,j)*eello_t3/fac_shield(j) + gshieldc_t3(k,iresshield-1)=gshieldc_t3(k,iresshield-1) + & +rlocshield + + enddo + enddo + + do k=1,3 + gshieldc_t3(k,i)=gshieldc_t3(k,i)+ + & grad_shield(k,i)*eello_t3/fac_shield(i) + gshieldc_t3(k,j)=gshieldc_t3(k,j)+ + & grad_shield(k,j)*eello_t3/fac_shield(j) + gshieldc_t3(k,i-1)=gshieldc_t3(k,i-1)+ + & grad_shield(k,i)*eello_t3/fac_shield(i) + gshieldc_t3(k,j-1)=gshieldc_t3(k,j-1)+ + & grad_shield(k,j)*eello_t3/fac_shield(j) + enddo + endif + +C if (energy_dec) write (iout,'(a6,2i5,0pf7.3)') cd write (2,*) 'i,',i,' j',j,'eello_turn3', cd & 0.5d0*(pizda(1,1)+pizda(2,2)), cd & ' eello_turn3_num',4*eello_turn3_num - if (calc_grad) then C Derivatives in gamma(i) call matmat2(EUgder(1,1,i+1),EUg(1,1,i+2),auxmat2(1,1)) - call transpose2(auxmat2(1,1),pizda(1,1)) - call matmat2(a_temp(1,1),pizda(1,1),pizda(1,1)) + call transpose2(auxmat2(1,1),auxmat3(1,1)) + call matmat2(a_temp(1,1),auxmat3(1,1),pizda(1,1)) gel_loc_turn3(i)=gel_loc_turn3(i)+0.5d0*(pizda(1,1)+pizda(2,2)) + & *fac_shield(i)*fac_shield(j) C Derivatives in gamma(i+1) call matmat2(EUg(1,1,i+1),EUgder(1,1,i+2),auxmat2(1,1)) - call transpose2(auxmat2(1,1),pizda(1,1)) - call matmat2(a_temp(1,1),pizda(1,1),pizda(1,1)) + call transpose2(auxmat2(1,1),auxmat3(1,1)) + call matmat2(a_temp(1,1),auxmat3(1,1),pizda(1,1)) gel_loc_turn3(i+1)=gel_loc_turn3(i+1) & +0.5d0*(pizda(1,1)+pizda(2,2)) + & *fac_shield(i)*fac_shield(j) C Cartesian derivatives do l=1,3 - a_temp(1,1)=aggi(l,1) - a_temp(1,2)=aggi(l,2) - a_temp(2,1)=aggi(l,3) - a_temp(2,2)=aggi(l,4) +c ghalf1=0.5d0*agg(l,1) +c ghalf2=0.5d0*agg(l,2) +c ghalf3=0.5d0*agg(l,3) +c ghalf4=0.5d0*agg(l,4) + a_temp(1,1)=aggi(l,1)!+ghalf1 + a_temp(1,2)=aggi(l,2)!+ghalf2 + a_temp(2,1)=aggi(l,3)!+ghalf3 + a_temp(2,2)=aggi(l,4)!+ghalf4 call matmat2(a_temp(1,1),auxmat1(1,1),pizda(1,1)) gcorr3_turn(l,i)=gcorr3_turn(l,i) & +0.5d0*(pizda(1,1)+pizda(2,2)) - a_temp(1,1)=aggi1(l,1) - a_temp(1,2)=aggi1(l,2) - a_temp(2,1)=aggi1(l,3) - a_temp(2,2)=aggi1(l,4) + & *fac_shield(i)*fac_shield(j) + + a_temp(1,1)=aggi1(l,1)!+agg(l,1) + a_temp(1,2)=aggi1(l,2)!+agg(l,2) + a_temp(2,1)=aggi1(l,3)!+agg(l,3) + a_temp(2,2)=aggi1(l,4)!+agg(l,4) call matmat2(a_temp(1,1),auxmat1(1,1),pizda(1,1)) gcorr3_turn(l,i+1)=gcorr3_turn(l,i+1) & +0.5d0*(pizda(1,1)+pizda(2,2)) - a_temp(1,1)=aggj(l,1) - a_temp(1,2)=aggj(l,2) - a_temp(2,1)=aggj(l,3) - a_temp(2,2)=aggj(l,4) + & *fac_shield(i)*fac_shield(j) + a_temp(1,1)=aggj(l,1)!+ghalf1 + a_temp(1,2)=aggj(l,2)!+ghalf2 + a_temp(2,1)=aggj(l,3)!+ghalf3 + a_temp(2,2)=aggj(l,4)!+ghalf4 call matmat2(a_temp(1,1),auxmat1(1,1),pizda(1,1)) gcorr3_turn(l,j)=gcorr3_turn(l,j) & +0.5d0*(pizda(1,1)+pizda(2,2)) + & *fac_shield(i)*fac_shield(j) a_temp(1,1)=aggj1(l,1) a_temp(1,2)=aggj1(l,2) a_temp(2,1)=aggj1(l,3) @@ -2554,9 +3610,45 @@ C Cartesian derivatives call matmat2(a_temp(1,1),auxmat1(1,1),pizda(1,1)) gcorr3_turn(l,j1)=gcorr3_turn(l,j1) & +0.5d0*(pizda(1,1)+pizda(2,2)) + & *fac_shield(i)*fac_shield(j) enddo - endif - else if (j.eq.i+3 .and. itype(i+2).ne.21) then + + endif ! calc_grad + + return + end +C------------------------------------------------------------------------------- + subroutine eturn4(i,eello_turn4) +C Third- and fourth-order contributions from turns + implicit real*8 (a-h,o-z) + include 'DIMENSIONS' + include 'COMMON.IOUNITS' + include 'COMMON.GEO' + include 'COMMON.VAR' + include 'COMMON.LOCAL' + include 'COMMON.CHAIN' + include 'COMMON.DERIV' + include 'COMMON.INTERACT' + include 'COMMON.CONTACTS' + include 'COMMON.TORSION' + include 'COMMON.VECTORS' + include 'COMMON.FFIELD' + include 'COMMON.CONTROL' + include 'COMMON.SHIELD' + dimension ggg(3) + double precision auxmat(2,2),auxmat1(2,2),auxmat2(2,2),pizda(2,2), + & e1t(2,2),e2t(2,2),e3t(2,2),e1tder(2,2),e2tder(2,2),e3tder(2,2), + & e1a(2,2),ae3(2,2),ae3e2(2,2),auxvec(2),auxvec1(2),auxgvec(2), + & auxgEvec1(2),auxgEvec2(2),auxgEvec3(2), + & gte1t(2,2),gte2t(2,2),gte3t(2,2), + & gte1a(2,2),gtae3(2,2),gtae3e2(2,2), ae3gte2(2,2), + & gtEpizda1(2,2),gtEpizda2(2,2),gtEpizda3(2,2) + double precision agg(3,4),aggi(3,4),aggi1(3,4), + & aggj(3,4),aggj1(3,4),a_temp(2,2),auxmat3(2,2) + common /locel/ a_temp,agg,aggi,aggi1,aggj,aggj1,a22,a23,a32,a33, + & dxi,dyi,dzi,dx_normi,dy_normi,dz_normi,xmedi,ymedi,zmedi, + & num_conti,j1,j2 + j=i+3 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC C C Fourth-order contributions @@ -2569,52 +3661,188 @@ C (i+1)o----i C CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC cd call checkint_turn4(i,a_temp,eello_turn4_num) - iti1=itortyp(itype(i+1)) - iti2=itortyp(itype(i+2)) - iti3=itortyp(itype(i+3)) +c write (iout,*) "eturn4 i",i," j",j," j1",j1," j2",j2 +c write(iout,*)"WCHODZE W PROGRAM" + a_temp(1,1)=a22 + a_temp(1,2)=a23 + a_temp(2,1)=a32 + a_temp(2,2)=a33 + iti1=itype2loc(itype(i+1)) + iti2=itype2loc(itype(i+2)) + iti3=itype2loc(itype(i+3)) +c write(iout,*) "iti1",iti1," iti2",iti2," iti3",iti3 call transpose2(EUg(1,1,i+1),e1t(1,1)) call transpose2(Eug(1,1,i+2),e2t(1,1)) call transpose2(Eug(1,1,i+3),e3t(1,1)) +C Ematrix derivative in theta + call transpose2(gtEUg(1,1,i+1),gte1t(1,1)) + call transpose2(gtEug(1,1,i+2),gte2t(1,1)) + call transpose2(gtEug(1,1,i+3),gte3t(1,1)) call matmat2(e1t(1,1),a_temp(1,1),e1a(1,1)) +c eta1 in derivative theta + call matmat2(gte1t(1,1),a_temp(1,1),gte1a(1,1)) call matvec2(e1a(1,1),Ub2(1,i+3),auxvec(1)) - s1=scalar2(b1(1,iti2),auxvec(1)) +c auxgvec is derivative of Ub2 so i+3 theta + call matvec2(e1a(1,1),gUb2(1,i+3),auxgvec(1)) +c auxalary matrix of E i+1 + call matvec2(gte1a(1,1),Ub2(1,i+3),auxgEvec1(1)) +c s1=0.0 +c gs1=0.0 + s1=scalar2(b1(1,i+2),auxvec(1)) +c derivative of theta i+2 with constant i+3 + gs23=scalar2(gtb1(1,i+2),auxvec(1)) +c derivative of theta i+2 with constant i+2 + gs32=scalar2(b1(1,i+2),auxgvec(1)) +c derivative of E matix in theta of i+1 + gsE13=scalar2(b1(1,i+2),auxgEvec1(1)) + call matmat2(a_temp(1,1),e3t(1,1),ae3(1,1)) +c ea31 in derivative theta + call matmat2(a_temp(1,1),gte3t(1,1),gtae3(1,1)) call matvec2(ae3(1,1),Ub2(1,i+2),auxvec(1)) - s2=scalar2(b1(1,iti1),auxvec(1)) +c auxilary matrix auxgvec of Ub2 with constant E matirx + call matvec2(ae3(1,1),gUb2(1,i+2),auxgvec(1)) +c auxilary matrix auxgEvec1 of E matix with Ub2 constant + call matvec2(gtae3(1,1),Ub2(1,i+2),auxgEvec3(1)) + +c s2=0.0 +c gs2=0.0 + s2=scalar2(b1(1,i+1),auxvec(1)) +c derivative of theta i+1 with constant i+3 + gs13=scalar2(gtb1(1,i+1),auxvec(1)) +c derivative of theta i+2 with constant i+1 + gs21=scalar2(b1(1,i+1),auxgvec(1)) +c derivative of theta i+3 with constant i+1 + gsE31=scalar2(b1(1,i+1),auxgEvec3(1)) +c write(iout,*) gs1,gs2,'i=',i,auxgvec(1),gUb2(1,i+2),gtb1(1,i+2), +c & gtb1(1,i+1) call matmat2(ae3(1,1),e2t(1,1),ae3e2(1,1)) +c two derivatives over diffetent matrices +c gtae3e2 is derivative over i+3 + call matmat2(gtae3(1,1),e2t(1,1),gtae3e2(1,1)) +c ae3gte2 is derivative over i+2 + call matmat2(ae3(1,1),gte2t(1,1),ae3gte2(1,1)) call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1)) +c three possible derivative over theta E matices +c i+1 + call matmat2(ae3e2(1,1),gte1t(1,1),gtEpizda1(1,1)) +c i+2 + call matmat2(ae3gte2(1,1),e1t(1,1),gtEpizda2(1,1)) +c i+3 + call matmat2(gtae3e2(1,1),e1t(1,1),gtEpizda3(1,1)) s3=0.5d0*(pizda(1,1)+pizda(2,2)) + + gsEE1=0.5d0*(gtEpizda1(1,1)+gtEpizda1(2,2)) + gsEE2=0.5d0*(gtEpizda2(1,1)+gtEpizda2(2,2)) + gsEE3=0.5d0*(gtEpizda3(1,1)+gtEpizda3(2,2)) + if (shield_mode.eq.0) then + fac_shield(i)=1.0 + fac_shield(j)=1.0 +C else +C fac_shield(i)=0.6 +C fac_shield(j)=0.4 + endif eello_turn4=eello_turn4-(s1+s2+s3) + & *fac_shield(i)*fac_shield(j) + eello_t4=-(s1+s2+s3) + & *fac_shield(i)*fac_shield(j) +c write(iout,*)'chujOWO', auxvec(1),b1(1,iti2) + if (energy_dec) write (iout,'(a6,2i5,0pf7.3,3f7.3)') + & 'eturn4',i,j,-(s1+s2+s3),s1,s2,s3 +C Now derivative over shield: + if ((fac_shield(i).gt.0).and.(fac_shield(j).gt.0).and. + & (shield_mode.gt.0)) then +C print *,i,j + + do ilist=1,ishield_list(i) + iresshield=shield_list(ilist,i) + do k=1,3 + rlocshield=grad_shield_side(k,ilist,i)*eello_t4/fac_shield(i) +C & *2.0 + gshieldx_t4(k,iresshield)=gshieldx_t4(k,iresshield)+ + & rlocshield + & +grad_shield_loc(k,ilist,i)*eello_t4/fac_shield(i) + gshieldc_t4(k,iresshield-1)=gshieldc_t4(k,iresshield-1) + & +rlocshield + enddo + enddo + do ilist=1,ishield_list(j) + iresshield=shield_list(ilist,j) + do k=1,3 + rlocshield=grad_shield_side(k,ilist,j)*eello_t4/fac_shield(j) +C & *2.0 + gshieldx_t4(k,iresshield)=gshieldx_t4(k,iresshield)+ + & rlocshield + & +grad_shield_loc(k,ilist,j)*eello_t4/fac_shield(j) + gshieldc_t4(k,iresshield-1)=gshieldc_t4(k,iresshield-1) + & +rlocshield + + enddo + enddo + + do k=1,3 + gshieldc_t4(k,i)=gshieldc_t4(k,i)+ + & grad_shield(k,i)*eello_t4/fac_shield(i) + gshieldc_t4(k,j)=gshieldc_t4(k,j)+ + & grad_shield(k,j)*eello_t4/fac_shield(j) + gshieldc_t4(k,i-1)=gshieldc_t4(k,i-1)+ + & grad_shield(k,i)*eello_t4/fac_shield(i) + gshieldc_t4(k,j-1)=gshieldc_t4(k,j-1)+ + & grad_shield(k,j)*eello_t4/fac_shield(j) + enddo + endif cd write (2,*) 'i,',i,' j',j,'eello_turn4',-(s1+s2+s3), cd & ' eello_turn4_num',8*eello_turn4_num +#ifdef NEWCORR + gloc(nphi+i,icg)=gloc(nphi+i,icg) + & -(gs13+gsE13+gsEE1)*wturn4 + & *fac_shield(i)*fac_shield(j) + gloc(nphi+i+1,icg)= gloc(nphi+i+1,icg) + & -(gs23+gs21+gsEE2)*wturn4 + & *fac_shield(i)*fac_shield(j) + + gloc(nphi+i+2,icg)= gloc(nphi+i+2,icg) + & -(gs32+gsE31+gsEE3)*wturn4 + & *fac_shield(i)*fac_shield(j) + +c gloc(nphi+i+1,icg)=gloc(nphi+i+1,icg)- +c & gs2 +#endif + if (energy_dec) write (iout,'(a6,2i5,0pf7.3)') + & 'eturn4',i,j,-(s1+s2+s3) +c write (iout,*) 'i,',i,' j',j,'eello_turn4',-(s1+s2+s3), +c & ' eello_turn4_num',8*eello_turn4_num C Derivatives in gamma(i) - if (calc_grad) then call transpose2(EUgder(1,1,i+1),e1tder(1,1)) call matmat2(e1tder(1,1),a_temp(1,1),auxmat(1,1)) call matvec2(auxmat(1,1),Ub2(1,i+3),auxvec(1)) - s1=scalar2(b1(1,iti2),auxvec(1)) + s1=scalar2(b1(1,i+2),auxvec(1)) call matmat2(ae3e2(1,1),e1tder(1,1),pizda(1,1)) s3=0.5d0*(pizda(1,1)+pizda(2,2)) gel_loc_turn4(i)=gel_loc_turn4(i)-(s1+s3) + & *fac_shield(i)*fac_shield(j) C Derivatives in gamma(i+1) call transpose2(EUgder(1,1,i+2),e2tder(1,1)) call matvec2(ae3(1,1),Ub2der(1,i+2),auxvec(1)) - s2=scalar2(b1(1,iti1),auxvec(1)) + s2=scalar2(b1(1,i+1),auxvec(1)) call matmat2(ae3(1,1),e2tder(1,1),auxmat(1,1)) call matmat2(auxmat(1,1),e1t(1,1),pizda(1,1)) s3=0.5d0*(pizda(1,1)+pizda(2,2)) gel_loc_turn4(i+1)=gel_loc_turn4(i+1)-(s2+s3) + & *fac_shield(i)*fac_shield(j) C Derivatives in gamma(i+2) call transpose2(EUgder(1,1,i+3),e3tder(1,1)) call matvec2(e1a(1,1),Ub2der(1,i+3),auxvec(1)) - s1=scalar2(b1(1,iti2),auxvec(1)) + s1=scalar2(b1(1,i+2),auxvec(1)) call matmat2(a_temp(1,1),e3tder(1,1),auxmat(1,1)) call matvec2(auxmat(1,1),Ub2(1,i+2),auxvec(1)) - s2=scalar2(b1(1,iti1),auxvec(1)) - call matmat2(auxmat(1,1),e2t(1,1),auxmat(1,1)) - call matmat2(auxmat(1,1),e1t(1,1),pizda(1,1)) + s2=scalar2(b1(1,i+1),auxvec(1)) + call matmat2(auxmat(1,1),e2t(1,1),auxmat3(1,1)) + call matmat2(auxmat3(1,1),e1t(1,1),pizda(1,1)) s3=0.5d0*(pizda(1,1)+pizda(2,2)) gel_loc_turn4(i+2)=gel_loc_turn4(i+2)-(s1+s2+s3) + & *fac_shield(i)*fac_shield(j) + if (calc_grad) then C Cartesian derivatives C Derivatives of this turn contributions in DC(i+2) if (j.lt.nres-1) then @@ -2625,15 +3853,16 @@ C Derivatives of this turn contributions in DC(i+2) a_temp(2,2)=agg(l,4) call matmat2(e1t(1,1),a_temp(1,1),e1a(1,1)) call matvec2(e1a(1,1),Ub2(1,i+3),auxvec(1)) - s1=scalar2(b1(1,iti2),auxvec(1)) + s1=scalar2(b1(1,i+2),auxvec(1)) call matmat2(a_temp(1,1),e3t(1,1),ae3(1,1)) call matvec2(ae3(1,1),Ub2(1,i+2),auxvec(1)) - s2=scalar2(b1(1,iti1),auxvec(1)) + s2=scalar2(b1(1,i+1),auxvec(1)) call matmat2(ae3(1,1),e2t(1,1),ae3e2(1,1)) call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1)) s3=0.5d0*(pizda(1,1)+pizda(2,2)) ggg(l)=-(s1+s2+s3) gcorr4_turn(l,i+2)=gcorr4_turn(l,i+2)-(s1+s2+s3) + & *fac_shield(i)*fac_shield(j) enddo endif C Remaining derivatives of this turn contribution @@ -2644,59 +3873,65 @@ C Remaining derivatives of this turn contribution a_temp(2,2)=aggi(l,4) call matmat2(e1t(1,1),a_temp(1,1),e1a(1,1)) call matvec2(e1a(1,1),Ub2(1,i+3),auxvec(1)) - s1=scalar2(b1(1,iti2),auxvec(1)) + s1=scalar2(b1(1,i+2),auxvec(1)) call matmat2(a_temp(1,1),e3t(1,1),ae3(1,1)) call matvec2(ae3(1,1),Ub2(1,i+2),auxvec(1)) - s2=scalar2(b1(1,iti1),auxvec(1)) + s2=scalar2(b1(1,i+1),auxvec(1)) call matmat2(ae3(1,1),e2t(1,1),ae3e2(1,1)) call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1)) s3=0.5d0*(pizda(1,1)+pizda(2,2)) gcorr4_turn(l,i)=gcorr4_turn(l,i)-(s1+s2+s3) + & *fac_shield(i)*fac_shield(j) a_temp(1,1)=aggi1(l,1) a_temp(1,2)=aggi1(l,2) a_temp(2,1)=aggi1(l,3) a_temp(2,2)=aggi1(l,4) call matmat2(e1t(1,1),a_temp(1,1),e1a(1,1)) call matvec2(e1a(1,1),Ub2(1,i+3),auxvec(1)) - s1=scalar2(b1(1,iti2),auxvec(1)) + s1=scalar2(b1(1,i+2),auxvec(1)) call matmat2(a_temp(1,1),e3t(1,1),ae3(1,1)) call matvec2(ae3(1,1),Ub2(1,i+2),auxvec(1)) - s2=scalar2(b1(1,iti1),auxvec(1)) + s2=scalar2(b1(1,i+1),auxvec(1)) call matmat2(ae3(1,1),e2t(1,1),ae3e2(1,1)) call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1)) s3=0.5d0*(pizda(1,1)+pizda(2,2)) gcorr4_turn(l,i+1)=gcorr4_turn(l,i+1)-(s1+s2+s3) + & *fac_shield(i)*fac_shield(j) a_temp(1,1)=aggj(l,1) a_temp(1,2)=aggj(l,2) a_temp(2,1)=aggj(l,3) a_temp(2,2)=aggj(l,4) call matmat2(e1t(1,1),a_temp(1,1),e1a(1,1)) call matvec2(e1a(1,1),Ub2(1,i+3),auxvec(1)) - s1=scalar2(b1(1,iti2),auxvec(1)) + s1=scalar2(b1(1,i+2),auxvec(1)) call matmat2(a_temp(1,1),e3t(1,1),ae3(1,1)) call matvec2(ae3(1,1),Ub2(1,i+2),auxvec(1)) - s2=scalar2(b1(1,iti1),auxvec(1)) + s2=scalar2(b1(1,i+1),auxvec(1)) call matmat2(ae3(1,1),e2t(1,1),ae3e2(1,1)) call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1)) s3=0.5d0*(pizda(1,1)+pizda(2,2)) gcorr4_turn(l,j)=gcorr4_turn(l,j)-(s1+s2+s3) + & *fac_shield(i)*fac_shield(j) a_temp(1,1)=aggj1(l,1) a_temp(1,2)=aggj1(l,2) a_temp(2,1)=aggj1(l,3) a_temp(2,2)=aggj1(l,4) call matmat2(e1t(1,1),a_temp(1,1),e1a(1,1)) call matvec2(e1a(1,1),Ub2(1,i+3),auxvec(1)) - s1=scalar2(b1(1,iti2),auxvec(1)) + s1=scalar2(b1(1,i+2),auxvec(1)) call matmat2(a_temp(1,1),e3t(1,1),ae3(1,1)) call matvec2(ae3(1,1),Ub2(1,i+2),auxvec(1)) - s2=scalar2(b1(1,iti1),auxvec(1)) + s2=scalar2(b1(1,i+1),auxvec(1)) call matmat2(ae3(1,1),e2t(1,1),ae3e2(1,1)) call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1)) s3=0.5d0*(pizda(1,1)+pizda(2,2)) +c write (iout,*) "s1",s1," s2",s2," s3",s3," s1+s2+s3",s1+s2+s3 gcorr4_turn(l,j1)=gcorr4_turn(l,j1)-(s1+s2+s3) + & *fac_shield(i)*fac_shield(j) enddo - endif - endif + + endif ! calc_grad + return end C----------------------------------------------------------------------------- @@ -2741,7 +3976,6 @@ C side-chain vectors. C implicit real*8 (a-h,o-z) include 'DIMENSIONS' - include 'sizesclu.dat' include 'COMMON.GEO' include 'COMMON.VAR' include 'COMMON.LOCAL' @@ -2757,7 +3991,7 @@ cd print '(a)','Enter ESCP' c write (iout,*) 'iatscp_s=',iatscp_s,' iatscp_e=',iatscp_e, c & ' scal14',scal14 do i=iatscp_s,iatscp_e - if (itype(i).eq.21 .or. itype(i+1).eq.21) cycle + if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle iteli=itel(i) c write (iout,*) "i",i," iteli",iteli," nscp_gr",nscp_gr(i), c & " iscp",(iscpstart(i,j),iscpend(i,j),j=1,nscp_gr(i)) @@ -2765,37 +3999,90 @@ c & " iscp",(iscpstart(i,j),iscpend(i,j),j=1,nscp_gr(i)) xi=0.5D0*(c(1,i)+c(1,i+1)) yi=0.5D0*(c(2,i)+c(2,i+1)) zi=0.5D0*(c(3,i)+c(3,i+1)) - +C Returning the ith atom to box + xi=mod(xi,boxxsize) + if (xi.lt.0) xi=xi+boxxsize + yi=mod(yi,boxysize) + if (yi.lt.0) yi=yi+boxysize + zi=mod(zi,boxzsize) + if (zi.lt.0) zi=zi+boxzsize do iint=1,nscp_gr(i) do j=iscpstart(i,iint),iscpend(i,iint) - itypj=itype(j) - if (itypj.eq.21) cycle + itypj=iabs(itype(j)) + if (itypj.eq.ntyp1) cycle C Uncomment following three lines for SC-p interactions c xj=c(1,nres+j)-xi c yj=c(2,nres+j)-yi c zj=c(3,nres+j)-zi C Uncomment following three lines for Ca-p interactions - xj=c(1,j)-xi - yj=c(2,j)-yi - zj=c(3,j)-zi + xj=c(1,j) + yj=c(2,j) + zj=c(3,j) +C returning the jth atom to box + xj=mod(xj,boxxsize) + if (xj.lt.0) xj=xj+boxxsize + yj=mod(yj,boxysize) + if (yj.lt.0) yj=yj+boxysize + zj=mod(zj,boxzsize) + if (zj.lt.0) zj=zj+boxzsize + dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2 + xj_safe=xj + yj_safe=yj + zj_safe=zj + subchap=0 +C Finding the closest jth atom + do xshift=-1,1 + do yshift=-1,1 + do zshift=-1,1 + xj=xj_safe+xshift*boxxsize + yj=yj_safe+yshift*boxysize + zj=zj_safe+zshift*boxzsize + dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2 + if(dist_temp.lt.dist_init) then + dist_init=dist_temp + xj_temp=xj + yj_temp=yj + zj_temp=zj + subchap=1 + endif + enddo + enddo + enddo + if (subchap.eq.1) then + xj=xj_temp-xi + yj=yj_temp-yi + zj=zj_temp-zi + else + xj=xj_safe-xi + yj=yj_safe-yi + zj=zj_safe-zi + endif rrij=1.0D0/(xj*xj+yj*yj+zj*zj) +C sss is scaling function for smoothing the cutoff gradient otherwise +C the gradient would not be continuouse + sss=sscale(1.0d0/(dsqrt(rrij))) + if (sss.le.0.0d0) cycle + sssgrad=sscagrad(1.0d0/(dsqrt(rrij))) fac=rrij**expon2 e1=fac*fac*aad(itypj,iteli) e2=fac*bad(itypj,iteli) if (iabs(j-i) .le. 2) then e1=scal14*e1 e2=scal14*e2 - evdw2_14=evdw2_14+e1+e2 + evdw2_14=evdw2_14+(e1+e2)*sss endif evdwij=e1+e2 -c write (iout,*) i,j,evdwij - evdw2=evdw2+evdwij +c write (iout,'(a6,2i5,0pf7.3,2i3,3e11.3)') +c & 'evdw2',i,j,evdwij,iteli,itypj,fac,aad(itypj,iteli), +c & bad(itypj,iteli) + evdw2=evdw2+evdwij*sss if (calc_grad) then C C Calculate contributions to the gradient in the virtual-bond and SC vectors. C - fac=-(evdwij+e1)*rrij + fac=-(evdwij+e1)*rrij*sss + fac=fac+(evdwij)*sssgrad*dsqrt(rrij)/expon ggg(1)=xj*fac ggg(2)=yj*fac ggg(3)=zj*fac @@ -2825,7 +4112,7 @@ cd write (iout,*) ggg(1),ggg(2),ggg(3) gvdwc_scp(l,k)=gvdwc_scp(l,k)-ggg(l) enddo enddo - endif + endif ! calc_grad enddo enddo ! iint 1225 continue @@ -2854,16 +4141,18 @@ C Evaluate bridge-strain energy and its gradient in virtual-bond and SC vectors. C implicit real*8 (a-h,o-z) include 'DIMENSIONS' - include 'sizesclu.dat' include 'COMMON.SBRIDGE' include 'COMMON.CHAIN' include 'COMMON.DERIV' include 'COMMON.VAR' include 'COMMON.INTERACT' + include 'COMMON.CONTROL' + include 'COMMON.IOUNITS' dimension ggg(3) ehpb=0.0D0 -cd print *,'edis: nhpb=',nhpb,' fbr=',fbr -cd print *,'link_start=',link_start,' link_end=',link_end +c write(iout,*)'edis: nhpb=',nhpb,' fbr=',fbr +c write(iout,*)'link_start=',link_start,' link_end=',link_end +C write(iout,*) link_end, "link_end" if (link_end.eq.0) return do i=link_start,link_end C If ihpb(i) and jhpb(i) > NRES, this is a SC-SC distance, otherwise a @@ -2880,24 +4169,98 @@ C iii and jjj point to the residues for which the distance is assigned. endif 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 +C if (ii.gt.nres .and. iabs(itype(iii)).eq.1 .and. +C & iabs(itype(jjj)).eq.1) then +C write(iout,*) constr_dist,"const" + if (.not.dyn_ss .and. i.le.nss) 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 - 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) + endif !ii.gt.neres + else if (ii.gt.nres .and. jj.gt.nres) then +c Restraints from contact prediction + dd=dist(ii,jj) + if (constr_dist.eq.11) then +C ehpb=ehpb+fordepth(i)**4.0d0 +C & *rlornmr1(dd,dhpb(i),dhpb1(i),forcon(i)) + ehpb=ehpb+fordepth(i)!**4.0d0 + & *rlornmr1(dd,dhpb(i),dhpb1(i),forcon(i)) + fac=fordepth(i)!**4.0d0 + & *rlornmr1prim(dd,dhpb(i),dhpb1(i),forcon(i))/dd +C write (iout,'(a6,2i5,3f8.3)') "edisl",ii,jj, +C & ehpb,fordepth(i),dd +C write(iout,*) ehpb,"atu?" +C ehpb,"tu?" +C fac=fordepth(i)**4.0d0 +C & *rlornmr1prim(dd,dhpb(i),dhpb1(i),forcon(i))/dd + else + 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 !end dhpb1(i).gt.0 + endif !end const_dist=11 + 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 !ii.gt.nres +C write(iout,*) "before" + dd=dist(ii,jj) +C write(iout,*) "after",dd + if (constr_dist.eq.11) then + ehpb=ehpb+fordepth(i)!**4.0d0 + & *rlornmr1(dd,dhpb(i),dhpb1(i),forcon(i)) + fac=fordepth(i)!**4.0d0 + & *rlornmr1prim(dd,dhpb(i),dhpb1(i),forcon(i))/dd +C ehpb=ehpb+fordepth(i)**4*rlornmr1(dd,dhpb(i),dhpb1(i)) +C fac=fordepth(i)**4*rlornmr1prim(dd,dhpb(i),dhpb1(i))/dd +C print *,ehpb,"tu?" +C write(iout,*) ehpb,"btu?", +C & dd,dhpb(i),dhpb1(i),fordepth(i),forcon(i) +C write (iout,'(a6,2i5,3f8.3)') "edisl",ii,jj, +C & ehpb,fordepth(i),dd + else + 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 -cd print *,'i=',i,' ii=',ii,' jj=',jj,' dhpb=',dhpb(i),' dd=',dd, -cd & ' waga=',waga,' fac=',fac + fac=waga*rdis/dd + endif + endif + do j=1,3 ggg(j)=fac*(c(j,jj)-c(j,ii)) enddo @@ -2917,7 +4280,7 @@ C Cartesian gradient in the SC vectors (ghpbx). enddo endif enddo - ehpb=0.5D0*ehpb + if (constr_dist.ne.11) ehpb=0.5D0*ehpb return end C-------------------------------------------------------------------------- @@ -2931,7 +4294,6 @@ C A. Liwo and U. Kozlowska, 11/24/03 C implicit real*8 (a-h,o-z) include 'DIMENSIONS' - include 'sizesclu.dat' include 'COMMON.SBRIDGE' include 'COMMON.CHAIN' include 'COMMON.DERIV' @@ -2940,7 +4302,7 @@ C 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) @@ -2948,7 +4310,7 @@ C 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 @@ -3012,7 +4374,6 @@ c Evaluate the energy of stretching of the CA-CA and CA-SC virtual bonds c implicit real*8 (a-h,o-z) include 'DIMENSIONS' - include 'sizesclu.dat' include 'COMMON.LOCAL' include 'COMMON.GEO' include 'COMMON.INTERACT' @@ -3023,40 +4384,48 @@ c include 'COMMON.NAMES' include 'COMMON.FFIELD' include 'COMMON.CONTROL' - logical energy_dec /.false./ double precision u(3),ud(3) estr=0.0d0 + estr1=0.0d0 +c write (iout,*) "distchainmax",distchainmax do i=nnt+1,nct - 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,vbld(i),distchainmax, +C & gnmr1(vbld(i),-1.0d0,distchainmax) +C else + if (itype(i-1).eq.ntyp1 .or. itype(i).eq.ntyp1) then + diff = vbld(i)-vbldpDUM +C write(iout,*) i,diff + else diff = vbld(i)-vbldp0 c write (iout,*) i,vbld(i),vbldp0,diff,AKP*diff*diff + endif estr=estr+diff*diff do j=1,3 gradb(j,i-1)=AKP*diff*dc(j,i-1)/vbld(i) enddo - endif - +C endif +C write (iout,'(a7,i5,4f7.3)') +C & "estr bb",i,vbld(i),vbldp0,diff,AKP*diff*diff enddo - estr=0.5d0*AKP*estr + 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=nnt,nct - 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) -c write (iout,*) i,iti,vbld(i+nres),vbldsc0(1,iti),diff, -c & AKSC(1,iti),AKSC(1,iti)*diff*diff +C write (iout,*) i,iti,vbld(i+nres),vbldsc0(1,iti),diff, +C & AKSC(1,iti),AKSC(1,iti)*diff*diff estr=estr+0.5d0*AKSC(1,iti)*diff*diff do j=1,3 gradbx(j,i)=AKSC(1,iti)*diff*dc(j,i+nres)/vbld(i+nres) @@ -3098,14 +4467,13 @@ c & AKSC(j,iti),abond0(j,iti),u(j),j=1,nbi) end #ifdef CRYST_THETA C-------------------------------------------------------------------------- - subroutine ebend(etheta) + subroutine ebend(etheta,ethetacnstr) C C Evaluate the virtual-bond-angle energy given the virtual-bond dihedral C angles gamma and its derivatives in consecutive thetas and gammas. C implicit real*8 (a-h,o-z) include 'DIMENSIONS' - include 'sizesclu.dat' include 'COMMON.LOCAL' include 'COMMON.GEO' include 'COMMON.INTERACT' @@ -3115,27 +4483,48 @@ C include 'COMMON.IOUNITS' include 'COMMON.NAMES' include 'COMMON.FFIELD' + include 'COMMON.TORCNSTR' common /calcthet/ term1,term2,termm,diffak,ratak, & ak,aktc,termpre,termexp,sigc,sig0i,time11,time12,sigcsq, & delthe0,sig0inv,sigtc,sigsqtc,delthec,it double precision y(2),z(2) delta=0.02d0*pi - time11=dexp(-2*time) - time12=1.0d0 +c time11=dexp(-2*time) +c time12=1.0d0 etheta=0.0D0 c write (iout,*) "nres",nres c write (*,'(a,i2)') 'EBEND ICG=',icg c write (iout,*) ithet_start,ithet_end do i=ithet_start,ithet_end - if (itype(i-1).eq.21) cycle +C if (itype(i-1).eq.ntyp1) cycle + if (i.le.2) 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.eq.3) then + y(1)=0.0D0 + y(2)=0.0D0 + else + + if (i.gt.3 .and. itype(i-3).ne.ntyp1) then #ifdef OSF phii=phi(i) - icrc=0 - call proc_proc(phii,icrc) +c icrc=0 +c call proc_proc(phii,icrc) if (icrc.eq.1) phii=150.0 #else phii=phi(i) @@ -3146,11 +4535,12 @@ C Zero the energy function and its derivative at 0 or pi. y(1)=0.0D0 y(2)=0.0D0 endif - if (i.lt.nres .and. itype(i).ne.21) then + endif + if (i.lt.nres .and. itype(i+1).ne.ntyp1) then #ifdef OSF phii1=phi(i+1) - icrc=0 - call proc_proc(phii1,icrc) +c icrc=0 +c call proc_proc(phii1,icrc) if (icrc.eq.1) phii1=150.0 phii1=pinorm(phii1) z(1)=cos(phii1) @@ -3168,8 +4558,12 @@ 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 c write (iout,*) "thet_pred_mean",thet_pred_mean @@ -3177,8 +4571,16 @@ c write (iout,*) "thet_pred_mean",thet_pred_mean 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) @@ -3201,12 +4603,41 @@ C Derivatives of the "mean" values in gamma1 and gamma2. & E_theta,E_tc) endif etheta=etheta+ethetai +c write (iout,'(a6,i5,0pf7.3,f7.3,i5)') +c & 'ebend',i,ethetai,theta(i),itype(i) c write (iout,'(2i3,3f8.3,f10.5)') i,it,rad2deg*theta(i), c & rad2deg*phii,rad2deg*phii1,ethetai 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) - 1215 continue +c 1215 continue + enddo + ethetacnstr=0.0d0 +C print *,ithetaconstr_start,ithetaconstr_end,"TU" + do i=1,ntheta_constr + itheta=itheta_constr(i) + thetiii=theta(itheta) + difi=pinorm(thetiii-theta_constr0(i)) + if (difi.gt.theta_drange(i)) then + difi=difi-theta_drange(i) + ethetacnstr=ethetacnstr+0.25d0*for_thet_constr(i)*difi**4 + gloc(itheta+nphi-2,icg)=gloc(itheta+nphi-2,icg) + & +for_thet_constr(i)*difi**3 + else if (difi.lt.-drange(i)) then + difi=difi+drange(i) + ethetacnstr=ethetacnstr+0.25d0*for_thet_constr(i)*difi**4 + gloc(itheta+nphi-2,icg)=gloc(itheta+nphi-2,icg) + & +for_thet_constr(i)*difi**3 + else + difi=0.0 + endif +C if (energy_dec) then +C write (iout,'(a6,2i5,4f8.3,2e14.5)') "ethetc", +C & i,itheta,rad2deg*thetiii, +C & rad2deg*theta_constr0(i), rad2deg*theta_drange(i), +C & rad2deg*difi,0.25d0*for_thet_constr(i)*difi**4, +C & gloc(itheta+nphi-2,icg) +C endif enddo C Ufff.... We've done all this!!! return @@ -3330,7 +4761,6 @@ c Kozlowska et al., J. Phys.: Condens. Matter 19 (2007) 285203 C implicit real*8 (a-h,o-z) include 'DIMENSIONS' - include 'sizesclu.dat' include 'COMMON.LOCAL' include 'COMMON.GEO' include 'COMMON.INTERACT' @@ -3341,6 +4771,7 @@ C include 'COMMON.NAMES' include 'COMMON.FFIELD' include 'COMMON.CONTROL' + include 'COMMON.TORCNSTR' double precision coskt(mmaxtheterm),sinkt(mmaxtheterm), & cosph1(maxsingle),sinph1(maxsingle),cosph2(maxsingle), & sinph2(maxsingle),cosph1ph2(maxdouble,maxdouble), @@ -3349,37 +4780,53 @@ C etheta=0.0D0 c write (iout,*) "ithetyp",(ithetyp(i),i=1,ntyp1) do i=ithet_start,ithet_end - if (itype(i-1).eq.21) cycle +C if (i.eq.2) cycle +C if (itype(i-1).eq.ntyp1) cycle + if (i.le.2) cycle + if ((itype(i-1).eq.ntyp1).or.itype(i-2).eq.ntyp1 + & .or.itype(i).eq.ntyp1) cycle + 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.eq.3) then + phii=0.0d0 + ityp1=nthetyp+1 + do k=1,nsingle + cosph1(k)=0.0d0 + sinph1(k)=0.0d0 + enddo + else + 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))) do k=1,nsingle cosph1(k)=dcos(k*phii) sinph1(k)=dsin(k*phii) enddo else phii=0.0d0 - ityp1=nthetyp+1 +c ityp1=nthetyp+1 do k=1,nsingle + ityp1=ithetyp((itype(i-2))) cosph1(k)=0.0d0 sinph1(k)=0.0d0 enddo endif - if (i.lt.nres .and. itype(i).ne.21) then + endif + if (i.lt.nres .and. itype(i+1).ne.ntyp1) then #ifdef OSF phii1=phi(i+1) if (phii1.ne.phii1) phii1=150.0 @@ -3387,14 +4834,15 @@ c write (iout,*) "ithetyp",(ithetyp(i),i=1,ntyp1) #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) enddo else phii1=0.0d0 - ityp3=nthetyp+1 +c ityp3=nthetyp+1 + ityp3=ithetyp((itype(i))) do k=1,nsingle cosph2(k)=0.0d0 sinph2(k)=0.0d0 @@ -3403,7 +4851,7 @@ c write (iout,*) "ithetyp",(ithetyp(i),i=1,ntyp1) 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) @@ -3425,11 +4873,12 @@ c call flush(iout) 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 @@ -3448,24 +4897,24 @@ c call flush(iout) 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) @@ -3473,28 +4922,29 @@ c call flush(iout) 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) @@ -3509,7 +4959,8 @@ c call flush(iout) 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 +c gloc(nphi+i-2,icg)=wang*dethetai + gloc(nphi+i-2,icg)=gloc(nphi+i-2,icg)+wang*dethetai enddo return end @@ -3522,7 +4973,6 @@ C corresponding virtual-bond valence angles THETA and the spherical angles C ALPHA and OMEGA. implicit real*8 (a-h,o-z) include 'DIMENSIONS' - include 'sizesclu.dat' include 'COMMON.GEO' include 'COMMON.LOCAL' include 'COMMON.VAR' @@ -3537,14 +4987,14 @@ C ALPHA and OMEGA. common /sccalc/ time11,time12,time112,theti,it,nlobit delta=0.02d0*pi escloc=0.0D0 -c write (iout,'(a)') 'ESC' +C write (iout,*) '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 +C write (iout,*) 'i=',i,' ssa=',ssa,' ssad=',ssad theti=theta(i+1)-pipol x(1)=dtan(theti) x(2)=alph(i) @@ -3580,8 +5030,8 @@ c write (iout,*) "i",i," x",x(1),x(2),x(3) dersc(k)=ss*dersc(k)+(1.0d0-ss)*dersc0(k) enddo dersc(2)=dersc(2)+ssd*(escloci-esclocbi) -c write (iout,*) 'i=',i,x(2)*rad2deg,escloci0,escloci, -c & esclocbi,ss,ssd + write (iout,*) 'i=',i,x(2)*rad2deg,escloci0,escloci, + & esclocbi,ss,ssd escloci=ss*escloci+(1.0d0-ss)*esclocbi c escloci=esclocbi c write (iout,*) escloci @@ -3615,15 +5065,17 @@ c write (iout,*) escloci enddo dersc(2)=dersc(2)+ssd*(escloci-esclocbi) c write (iout,*) 'i=',i,x(2)*rad2deg,escloci0,escloci, -c & esclocbi,ss,ssd +c & esclocbi,ss,ssd escloci=ss*escloci+(1.0d0-ss)*esclocbi -c write (iout,*) escloci +C write (iout,*) 'i=',i, escloci else call enesc(x,escloci,dersc,ddummy,.false.) endif escloc=escloc+escloci -c write (iout,*) 'i=',i,' escloci=',escloci,' dersc=',dersc +C write (iout,*) 'i=',i,' escloci=',escloci,' dersc=',dersc + write (iout,'(a6,i5,0pf7.3)') + & 'escloc',i,escloci gloc(nphi+i-1,icg)=gloc(nphi+i-1,icg)+ & wscloc*dersc(1) @@ -3697,7 +5149,7 @@ C Compute the contribution to SC energy and derivatives 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 @@ -3778,7 +5230,7 @@ C Compute the contribution to SC energy and derivatives 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 @@ -3807,7 +5259,6 @@ C added by Urszula Kozlowska. 07/11/2007 C implicit real*8 (a-h,o-z) include 'DIMENSIONS' - include 'sizesclu.dat' include 'COMMON.GEO' include 'COMMON.LOCAL' include 'COMMON.VAR' @@ -3833,7 +5284,7 @@ C 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))) @@ -3842,7 +5293,7 @@ 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 @@ -3860,7 +5311,7 @@ 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) @@ -3892,7 +5343,7 @@ 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 @@ -3900,7 +5351,7 @@ 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(1.0d0,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 @@ -3943,6 +5394,8 @@ c & dscp1,dscp2,sumene c sumene = enesc(x,xx,yy,zz,cost2tab(i+1),sint2tab(i+1)) escloc = escloc + sumene c write (2,*) "escloc",escloc +c write (2,*) "i",i," escloc",sumene,escloc,it,itype(i), +c & zz,xx,yy if (.not. calc_grad) goto 1 #ifdef DEBUG C @@ -4071,8 +5524,10 @@ 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)) @@ -4158,7 +5613,6 @@ c------------------------------------------------------------------------------ subroutine splinthet(theti,delta,ss,ssder) implicit real*8 (a-h,o-z) include 'DIMENSIONS' - include 'sizesclu.dat' include 'COMMON.VAR' include 'COMMON.GEO' thetup=pi-delta @@ -4203,10 +5657,9 @@ c------------------------------------------------------------------------------ C----------------------------------------------------------------------------- #ifdef CRYST_TOR C----------------------------------------------------------------------------- - subroutine etor(etors,edihcnstr,fact) + subroutine etor(etors,fact) implicit real*8 (a-h,o-z) include 'DIMENSIONS' - include 'sizesclu.dat' include 'COMMON.VAR' include 'COMMON.GEO' include 'COMMON.LOCAL' @@ -4224,8 +5677,8 @@ C Set lprn=.true. for debugging 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 + if (itype(i-2).eq.ntyp1 .or. itype(i-1).eq.ntyp1 + & .or. itype(i).eq.ntyp1) cycle itori=itortyp(itype(i-2)) itori1=itortyp(itype(i-1)) phii=phi(i) @@ -4265,33 +5718,13 @@ C Proline-Proline pair is a special case... gloc(i-3,icg)=gloc(i-3,icg)+wtor*fact*gloci c write (iout,*) 'i=',i,' gloc=',gloc(i-3,icg) enddo -! 6/20/98 - dihedral angle constraints - edihcnstr=0.0d0 - do i=1,ndih_constr - itori=idih_constr(i) - phii=phi(itori) - difi=phii-phi0(i) - if (difi.gt.drange(i)) then - difi=difi-drange(i) - edihcnstr=edihcnstr+0.25d0*ftors*difi**4 - gloc(itori-3,icg)=gloc(itori-3,icg)+ftors*difi**3 - else if (difi.lt.-drange(i)) then - difi=difi+drange(i) - edihcnstr=edihcnstr+0.25d0*ftors*difi**4 - gloc(itori-3,icg)=gloc(itori-3,icg)+ftors*difi**3 - endif -! write (iout,'(2i5,2f8.3,2e14.5)') i,itori,rad2deg*phii, -! & rad2deg*difi,0.25d0*ftors*difi**4,gloc(itori-3,icg) - enddo -! write (iout,*) 'edihcnstr',edihcnstr return end c------------------------------------------------------------------------------ #else - subroutine etor(etors,edihcnstr,fact) + subroutine etor(etors,fact) implicit real*8 (a-h,o-z) include 'DIMENSIONS' - include 'sizesclu.dat' include 'COMMON.VAR' include 'COMMON.GEO' include 'COMMON.LOCAL' @@ -4309,17 +5742,25 @@ C Set lprn=.true. for debugging 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 + if (i.le.2) 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 if (itype(i-2).eq.ntyp1 .or. itype(i-1).eq.ntyp1 +C & .or. itype(i).eq.ntyp1) cycle 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 @@ -4332,52 +5773,28 @@ C [v2 cos(phi/2)+v3 sin(phi/2)]^2 + 1 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) pom=vl2ij*cosphi+vl3ij*sinphi pom1=1.0d0/(pom*pom+1.0d0) etors=etors+vl1ij*pom1 +c if (energy_dec) etors_ii=etors_ii+ +c & vl1ij*pom1 pom=-pom*pom1*pom1 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 enddo -! 6/20/98 - dihedral angle constraints - edihcnstr=0.0d0 - do i=1,ndih_constr - itori=idih_constr(i) - phii=phi(itori) - difi=pinorm(phii-phi0(i)) - edihi=0.0d0 - if (difi.gt.drange(i)) then - difi=difi-drange(i) - edihcnstr=edihcnstr+0.25d0*ftors*difi**4 - gloc(itori-3,icg)=gloc(itori-3,icg)+ftors*difi**3 - edihi=0.25d0*ftors*difi**4 - else if (difi.lt.-drange(i)) then - difi=difi+drange(i) - edihcnstr=edihcnstr+0.25d0*ftors*difi**4 - gloc(itori-3,icg)=gloc(itori-3,icg)+ftors*difi**3 - edihi=0.25d0*ftors*difi**4 - else - difi=0.0d0 - endif -c write (iout,'(2i5,4f10.5,e15.5)') i,itori,phii,phi0(i),difi, -c & drange(i),edihi -! write (iout,'(2i5,2f8.3,2e14.5)') i,itori,rad2deg*phii, -! & rad2deg*difi,0.25d0*ftors*difi**4,gloc(itori-3,icg) - enddo -! write (iout,*) 'edihcnstr',edihcnstr return end c---------------------------------------------------------------------------- @@ -4385,7 +5802,6 @@ c---------------------------------------------------------------------------- C 6/23/01 Compute double torsional energy implicit real*8 (a-h,o-z) include 'DIMENSIONS' - include 'sizesclu.dat' include 'COMMON.VAR' include 'COMMON.GEO' include 'COMMON.LOCAL' @@ -4403,8 +5819,12 @@ C Set lprn=.true. for debugging c lprn=.true. etors_d=0.0D0 do i=iphi_start,iphi_end-1 - if (itype(i-2).eq.21 .or. itype(i-1).eq.21 - & .or. itype(i).eq.21 .or. itype(i+1).eq.21) cycle + if (i.le.3) cycle +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 + 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 if (itel(i-2).eq.0 .or. itel(i-1).eq.0 .or. itel(i).eq.0) & goto 1215 itori=itortyp(itype(i-2)) @@ -4414,12 +5834,14 @@ 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) + 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) @@ -4429,12 +5851,12 @@ C Regular cosine and sine terms 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) @@ -4444,7 +5866,7 @@ C Regular cosine and sine terms gloci1=gloci1+l*(v1sdij*cosphi1p2+v2sdij*cosphi1m2 & -v1cdij*sinphi1p2-v2cdij*sinphi1m2) gloci2=gloci2+(k-l)*(v1sdij*cosphi1p2-v2sdij*cosphi1m2 - & -v1cdij*sinphi1p2+v2cdij*sinphi1m2) + & -v1cdij*sinphi1p2+v2cdij*sinphi1m2) enddo enddo gloc(i-3,icg)=gloc(i-3,icg)+wtor_d*fact2*gloci1 @@ -4454,6 +5876,286 @@ C Regular cosine and sine terms return end #endif +c--------------------------------------------------------------------------- +C The rigorous attempt to derive energy function + subroutine etor_kcc(etors,fact) + implicit real*8 (a-h,o-z) + include 'DIMENSIONS' + include 'COMMON.VAR' + include 'COMMON.GEO' + include 'COMMON.LOCAL' + include 'COMMON.TORSION' + include 'COMMON.INTERACT' + include 'COMMON.DERIV' + include 'COMMON.CHAIN' + include 'COMMON.NAMES' + include 'COMMON.IOUNITS' + include 'COMMON.FFIELD' + include 'COMMON.TORCNSTR' + include 'COMMON.CONTROL' + double precision c1(0:maxval_kcc),c2(0:maxval_kcc) + logical lprn +c double precision thybt1(maxtermkcc),thybt2(maxtermkcc) +C Set lprn=.true. for debugging + lprn=energy_dec +c lprn=.true. +C print *,"wchodze kcc" + if (lprn) write (iout,*) "etor_kcc tor_mode",tor_mode + etors=0.0D0 + do i=iphi_start,iphi_end +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 + itori=itortyp(itype(i-2)) + itori1=itortyp(itype(i-1)) + phii=phi(i) + glocig=0.0D0 + glocit1=0.0d0 + glocit2=0.0d0 +C to avoid multiple devision by 2 +c theti22=0.5d0*theta(i) +C theta 12 is the theta_1 /2 +C theta 22 is theta_2 /2 +c theti12=0.5d0*theta(i-1) +C and appropriate sinus function + sinthet1=dsin(theta(i-1)) + sinthet2=dsin(theta(i)) + costhet1=dcos(theta(i-1)) + costhet2=dcos(theta(i)) +C to speed up lets store its mutliplication + sint1t2=sinthet2*sinthet1 + sint1t2n=1.0d0 +C \sum_{i=1}^n (sin(theta_1) * sin(theta_2))^n * (c_n* cos(n*gamma) +C +d_n*sin(n*gamma)) * +C \sum_{i=1}^m (1+a_m*Tb_m(cos(theta_1 /2))+b_m*Tb_m(cos(theta_2 /2))) +C we have two sum 1) Non-Chebyshev which is with n and gamma + nval=nterm_kcc_Tb(itori,itori1) + c1(0)=0.0d0 + c2(0)=0.0d0 + c1(1)=1.0d0 + c2(1)=1.0d0 + do j=2,nval + c1(j)=c1(j-1)*costhet1 + c2(j)=c2(j-1)*costhet2 + enddo + etori=0.0d0 + do j=1,nterm_kcc(itori,itori1) + cosphi=dcos(j*phii) + sinphi=dsin(j*phii) + sint1t2n1=sint1t2n + sint1t2n=sint1t2n*sint1t2 + sumvalc=0.0d0 + gradvalct1=0.0d0 + gradvalct2=0.0d0 + do k=1,nval + do l=1,nval + sumvalc=sumvalc+v1_kcc(l,k,j,itori1,itori)*c1(k)*c2(l) + gradvalct1=gradvalct1+ + & (k-1)*v1_kcc(l,k,j,itori1,itori)*c1(k-1)*c2(l) + gradvalct2=gradvalct2+ + & (l-1)*v1_kcc(l,k,j,itori1,itori)*c1(k)*c2(l-1) + enddo + enddo + gradvalct1=-gradvalct1*sinthet1 + gradvalct2=-gradvalct2*sinthet2 + sumvals=0.0d0 + gradvalst1=0.0d0 + gradvalst2=0.0d0 + do k=1,nval + do l=1,nval + sumvals=sumvals+v2_kcc(l,k,j,itori1,itori)*c1(k)*c2(l) + gradvalst1=gradvalst1+ + & (k-1)*v2_kcc(l,k,j,itori1,itori)*c1(k-1)*c2(l) + gradvalst2=gradvalst2+ + & (l-1)*v2_kcc(l,k,j,itori1,itori)*c1(k)*c2(l-1) + enddo + enddo + gradvalst1=-gradvalst1*sinthet1 + gradvalst2=-gradvalst2*sinthet2 + etori=etori+sint1t2n*(sumvalc*cosphi+sumvals*sinphi) +C glocig is the gradient local i site in gamma + glocig=glocig+j*sint1t2n*(sumvals*cosphi-sumvalc*sinphi) +C now gradient over theta_1 + glocit1=glocit1+sint1t2n*(gradvalct1*cosphi+gradvalst1*sinphi) + & +j*sint1t2n1*costhet1*sinthet2*(sumvalc*cosphi+sumvals*sinphi) + glocit2=glocit2+sint1t2n*(gradvalct2*cosphi+gradvalst2*sinphi) + & +j*sint1t2n1*sinthet1*costhet2*(sumvalc*cosphi+sumvals*sinphi) + enddo ! j + etors=etors+etori +C derivative over gamma + gloc(i-3,icg)=gloc(i-3,icg)+wtor*glocig +C derivative over theta1 + gloc(nphi+i-3,icg)=gloc(nphi+i-3,icg)+wtor*glocit1 +C now derivative over theta2 + gloc(nphi+i-2,icg)=gloc(nphi+i-2,icg)+wtor*glocit2 + if (lprn) + & write (iout,*) i-2,i-1,itype(i-2),itype(i-1),itori,itori1, + & theta(i-1)*rad2deg,theta(i)*rad2deg,phii*rad2deg,etori + enddo + return + end +c--------------------------------------------------------------------------------------------- + subroutine etor_constr(edihcnstr) + implicit real*8 (a-h,o-z) + include 'DIMENSIONS' + include 'COMMON.VAR' + include 'COMMON.GEO' + include 'COMMON.LOCAL' + include 'COMMON.TORSION' + include 'COMMON.INTERACT' + include 'COMMON.DERIV' + include 'COMMON.CHAIN' + include 'COMMON.NAMES' + include 'COMMON.IOUNITS' + include 'COMMON.FFIELD' + include 'COMMON.TORCNSTR' + include 'COMMON.CONTROL' +! 6/20/98 - dihedral angle constraints + edihcnstr=0.0d0 +c do i=1,ndih_constr +c write (iout,*) "idihconstr_start",idihconstr_start, +c & " idihconstr_end",idihconstr_end + if (raw_psipred) then + do i=idihconstr_start,idihconstr_end + itori=idih_constr(i) + phii=phi(itori) + gaudih_i=vpsipred(1,i) + gauder_i=0.0d0 + do j=1,2 + s = sdihed(j,i) + cos_i=(1.0d0-dcos(phii-phibound(j,i)))/s**2 + dexpcos_i=dexp(-cos_i*cos_i) + gaudih_i=gaudih_i+vpsipred(j+1,i)*dexpcos_i + gauder_i=gauder_i-2*vpsipred(j+1,i)*dsin(phii-phibound(j,i)) + & *cos_i*dexpcos_i/s**2 + enddo + edihcnstr=edihcnstr-wdihc*dlog(gaudih_i) + gloc(itori-3,icg)=gloc(itori-3,icg)-wdihc*gauder_i/gaudih_i + if (energy_dec) + & write (iout,'(2i5,f8.3,f8.5,2(f8.5,2f8.3),f10.5)') + & i,itori,phii*rad2deg,vpsipred(1,i),vpsipred(2,i), + & phibound(1,i)*rad2deg,sdihed(1,i)*rad2deg,vpsipred(3,i), + & phibound(2,i)*rad2deg,sdihed(2,i)*rad2deg, + & -wdihc*dlog(gaudih_i) + enddo + else + do i=idihconstr_start,idihconstr_end + itori=idih_constr(i) + phii=phi(itori) + difi=pinorm(phii-phi0(i)) + if (difi.gt.drange(i)) then + difi=difi-drange(i) + edihcnstr=edihcnstr+0.25d0*ftors(i)*difi**4 + gloc(itori-3,icg)=gloc(itori-3,icg)+ftors(i)*difi**3 + else if (difi.lt.-drange(i)) then + difi=difi+drange(i) + edihcnstr=edihcnstr+0.25d0*ftors(i)*difi**4 + gloc(itori-3,icg)=gloc(itori-3,icg)+ftors(i)*difi**3 + else + difi=0.0 + endif + enddo + endif + return + end +c---------------------------------------------------------------------------- +C The rigorous attempt to derive energy function + subroutine ebend_kcc(etheta) + + implicit real*8 (a-h,o-z) + include 'DIMENSIONS' + include 'COMMON.VAR' + include 'COMMON.GEO' + include 'COMMON.LOCAL' + include 'COMMON.TORSION' + include 'COMMON.INTERACT' + include 'COMMON.DERIV' + include 'COMMON.CHAIN' + include 'COMMON.NAMES' + include 'COMMON.IOUNITS' + include 'COMMON.FFIELD' + include 'COMMON.TORCNSTR' + include 'COMMON.CONTROL' + logical lprn + double precision thybt1(maxang_kcc) +C Set lprn=.true. for debugging + lprn=energy_dec +c lprn=.true. +C print *,"wchodze kcc" + if (lprn) write (iout,*) "ebend_kcc tor_mode",tor_mode + etheta=0.0D0 + do i=ithet_start,ithet_end +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 + iti=iabs(itortyp(itype(i-1))) + sinthet=dsin(theta(i)) + costhet=dcos(theta(i)) + do j=1,nbend_kcc_Tb(iti) + thybt1(j)=v1bend_chyb(j,iti) + enddo + sumth1thyb=v1bend_chyb(0,iti)+ + & tschebyshev(1,nbend_kcc_Tb(iti),thybt1(1),costhet) + if (lprn) write (iout,*) i-1,itype(i-1),iti,theta(i)*rad2deg, + & sumth1thyb + ihelp=nbend_kcc_Tb(iti)-1 + gradthybt1=gradtschebyshev(0,ihelp,thybt1(1),costhet) + etheta=etheta+sumth1thyb +C print *,sumth1thyb,gradthybt1,sinthet*(-0.5d0) + gloc(nphi+i-2,icg)=gloc(nphi+i-2,icg)-wang*gradthybt1*sinthet + enddo + return + end +c------------------------------------------------------------------------------------- + subroutine etheta_constr(ethetacnstr) + + implicit real*8 (a-h,o-z) + include 'DIMENSIONS' + include 'COMMON.VAR' + include 'COMMON.GEO' + include 'COMMON.LOCAL' + include 'COMMON.TORSION' + include 'COMMON.INTERACT' + include 'COMMON.DERIV' + include 'COMMON.CHAIN' + include 'COMMON.NAMES' + include 'COMMON.IOUNITS' + include 'COMMON.FFIELD' + include 'COMMON.TORCNSTR' + include 'COMMON.CONTROL' + ethetacnstr=0.0d0 +C print *,ithetaconstr_start,ithetaconstr_end,"TU" + do i=ithetaconstr_start,ithetaconstr_end + itheta=itheta_constr(i) + thetiii=theta(itheta) + difi=pinorm(thetiii-theta_constr0(i)) + if (difi.gt.theta_drange(i)) then + difi=difi-theta_drange(i) + ethetacnstr=ethetacnstr+0.25d0*for_thet_constr(i)*difi**4 + gloc(itheta+nphi-2,icg)=gloc(itheta+nphi-2,icg) + & +for_thet_constr(i)*difi**3 + else if (difi.lt.-drange(i)) then + difi=difi+drange(i) + ethetacnstr=ethetacnstr+0.25d0*for_thet_constr(i)*difi**4 + gloc(itheta+nphi-2,icg)=gloc(itheta+nphi-2,icg) + & +for_thet_constr(i)*difi**3 + else + difi=0.0 + endif + if (energy_dec) then + write (iout,'(a6,2i5,4f8.3,2e14.5)') "ethetc", + & i,itheta,rad2deg*thetiii, + & rad2deg*theta_constr0(i), rad2deg*theta_drange(i), + & rad2deg*difi,0.25d0*for_thet_constr(i)*difi**4, + & gloc(itheta+nphi-2,icg) + endif + enddo + return + end +c------------------------------------------------------------------------------ c------------------------------------------------------------------------------ subroutine eback_sc_corr(esccor) c 7/21/2007 Correlations between the backbone-local and side-chain-local @@ -4464,7 +6166,6 @@ c of residues computed from AM1 energy surfaces of terminally-blocked c amino-acid residues. implicit real*8 (a-h,o-z) include 'DIMENSIONS' - include 'sizesclu.dat' include 'COMMON.VAR' include 'COMMON.GEO' include 'COMMON.LOCAL' @@ -4483,26 +6184,50 @@ C Set lprn=.true. for debugging c lprn=.true. c write (iout,*) "EBACK_SC_COR",iphi_start,iphi_end,nterm_sccor 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)) 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) - esccor=esccor+v1ij*cosphi+v2ij*sinphi - gloci=gloci+j*(v2ij*cosphi-v1ij*sinphi) - enddo + 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",esccor,i +c write (iout,*) "EBACK_SC_COR",i,v1ij*cosphi+v2ij*sinphi,intertyp, +c & nterm_sccor(isccori,isccori1),isccori,isccori1 +c 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) - gsccor_loc(i-3)=gloci + & (v1sccor(j,1,itori,itori1),j=1,6) + & ,(v2sccor(j,1,itori,itori1),j=1,6) +c gsccor_loc(i-3)=gloci + enddo !intertyp enddo return end @@ -4604,192 +6329,20 @@ cd & k,l,(gacont(m,kk,k),m=1,3) return end c------------------------------------------------------------------------------ -#ifdef MPL - subroutine pack_buffer(dimen1,dimen2,atom,indx,buffer) - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' - 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) - num_kont=num_cont_hb(atom) - do i=1,num_kont - do k=1,7 - do j=1,3 - buffer(i,indx+(k-1)*3+j)=zapas(j,i,atom,k) - enddo ! j - enddo ! k - buffer(i,indx+22)=facont_hb(i,atom) - buffer(i,indx+23)=ees0p(i,atom) - buffer(i,indx+24)=ees0m(i,atom) - buffer(i,indx+25)=dfloat(jcont_hb(i,atom)) - enddo ! i - buffer(1,indx+26)=dfloat(num_kont) - return - end -c------------------------------------------------------------------------------ - subroutine unpack_buffer(dimen1,dimen2,atom,indx,buffer) - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' - 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) - num_kont=buffer(1,indx+26) - num_kont_old=num_cont_hb(atom) - num_cont_hb(atom)=num_kont+num_kont_old - do i=1,num_kont - ii=i+num_kont_old - do k=1,7 - do j=1,3 - zapas(j,ii,atom,k)=buffer(i,indx+(k-1)*3+j) - enddo ! j - enddo ! k - facont_hb(ii,atom)=buffer(i,indx+22) - ees0p(ii,atom)=buffer(i,indx+23) - ees0m(ii,atom)=buffer(i,indx+24) - jcont_hb(ii,atom)=buffer(i,indx+25) - enddo ! i - return - end -c------------------------------------------------------------------------------ -#endif subroutine multibody_hb(ecorr,ecorr5,ecorr6,n_corr,n_corr1) C This subroutine calculates multi-body contributions to hydrogen-bonding implicit real*8 (a-h,o-z) include 'DIMENSIONS' - include 'sizesclu.dat' include 'COMMON.IOUNITS' -#ifdef MPL - include 'COMMON.INFO' -#endif include 'COMMON.FFIELD' include 'COMMON.DERIV' include 'COMMON.INTERACT' include 'COMMON.CONTACTS' -#ifdef MPL - parameter (max_cont=maxconts) - parameter (max_dim=2*(8*3+2)) - parameter (msglen1=max_cont*max_dim*4) - parameter (msglen2=2*msglen1) - integer source,CorrelType,CorrelID,Error - double precision buffer(max_cont,max_dim) -#endif double precision gx(3),gx1(3) logical lprn,ldone C Set lprn=.true. for debugging lprn=.false. -#ifdef MPL - n_corr=0 - n_corr1=0 - if (fgProcs.le.1) goto 30 - if (lprn) then - write (iout,'(a)') 'Contact function values:' - do i=nnt,nct-2 - write (iout,'(2i3,50(1x,i2,f5.2))') - & i,num_cont_hb(i),(jcont_hb(j,i),facont_hb(j,i), - & j=1,num_cont_hb(i)) - enddo - endif -C Caution! Following code assumes that electrostatic interactions concerning -C a given atom are split among at most two processors! - CorrelType=477 - CorrelID=MyID+1 - ldone=.false. - do i=1,max_cont - do j=1,max_dim - buffer(i,j)=0.0D0 - enddo - enddo - mm=mod(MyRank,2) -cd write (iout,*) 'MyRank',MyRank,' mm',mm - if (mm) 20,20,10 - 10 continue -cd write (iout,*) 'Sending: MyRank',MyRank,' mm',mm,' ldone',ldone - if (MyRank.gt.0) then -C Send correlation contributions to the preceding processor - msglen=msglen1 - nn=num_cont_hb(iatel_s) - call pack_buffer(max_cont,max_dim,iatel_s,0,buffer) -cd write (iout,*) 'The BUFFER array:' -cd do i=1,nn -cd write (iout,'(i2,9(3f8.3,2x))') i,(buffer(i,j),j=1,26) -cd enddo - if (ielstart(iatel_s).gt.iatel_s+ispp) then - msglen=msglen2 - call pack_buffer(max_cont,max_dim,iatel_s+1,26,buffer) -C Clear the contacts of the atom passed to the neighboring processor - nn=num_cont_hb(iatel_s+1) -cd do i=1,nn -cd write (iout,'(i2,9(3f8.3,2x))') i,(buffer(i,j+26),j=1,26) -cd enddo - num_cont_hb(iatel_s)=0 - endif -cd write (iout,*) 'Processor ',MyID,MyRank, -cd & ' is sending correlation contribution to processor',MyID-1, -cd & ' msglen=',msglen -cd write (*,*) 'Processor ',MyID,MyRank, -cd & ' is sending correlation contribution to processor',MyID-1, -cd & ' msglen=',msglen,' CorrelType=',CorrelType - call mp_bsend(buffer,msglen,MyID-1,CorrelType,CorrelID) -cd write (iout,*) 'Processor ',MyID, -cd & ' has sent correlation contribution to processor',MyID-1, -cd & ' msglen=',msglen,' CorrelID=',CorrelID -cd write (*,*) 'Processor ',MyID, -cd & ' has sent correlation contribution to processor',MyID-1, -cd & ' msglen=',msglen,' CorrelID=',CorrelID - msglen=msglen1 - endif ! (MyRank.gt.0) - if (ldone) goto 30 - ldone=.true. - 20 continue -cd write (iout,*) 'Receiving: MyRank',MyRank,' mm',mm,' ldone',ldone - if (MyRank.lt.fgProcs-1) then -C Receive correlation contributions from the next processor - msglen=msglen1 - if (ielend(iatel_e).lt.nct-1) msglen=msglen2 -cd write (iout,*) 'Processor',MyID, -cd & ' is receiving correlation contribution from processor',MyID+1, -cd & ' msglen=',msglen,' CorrelType=',CorrelType -cd write (*,*) 'Processor',MyID, -cd & ' is receiving correlation contribution from processor',MyID+1, -cd & ' msglen=',msglen,' CorrelType=',CorrelType - nbytes=-1 - do while (nbytes.le.0) - call mp_probe(MyID+1,CorrelType,nbytes) - enddo -cd print *,'Processor',MyID,' msglen',msglen,' nbytes',nbytes - call mp_brecv(buffer,msglen,MyID+1,CorrelType,nbytes) -cd write (iout,*) 'Processor',MyID, -cd & ' has received correlation contribution from processor',MyID+1, -cd & ' msglen=',msglen,' nbytes=',nbytes -cd write (iout,*) 'The received BUFFER array:' -cd do i=1,max_cont -cd write (iout,'(i2,9(3f8.3,2x))') i,(buffer(i,j),j=1,52) -cd enddo - if (msglen.eq.msglen1) then - call unpack_buffer(max_cont,max_dim,iatel_e+1,0,buffer) - else if (msglen.eq.msglen2) then - call unpack_buffer(max_cont,max_dim,iatel_e,0,buffer) - call unpack_buffer(max_cont,max_dim,iatel_e+1,26,buffer) - else - write (iout,*) - & 'ERROR!!!! message length changed while processing correlations.' - write (*,*) - & 'ERROR!!!! message length changed while processing correlations.' - call mp_stopall(Error) - endif ! msglen.eq.msglen1 - endif ! MyRank.lt.fgProcs-1 - if (ldone) goto 30 - ldone=.true. - goto 10 - 30 continue -#endif if (lprn) then write (iout,'(a)') 'Contact function values:' do i=nnt,nct-2 @@ -4848,141 +6401,32 @@ c------------------------------------------------------------------------------ C This subroutine calculates multi-body contributions to hydrogen-bonding implicit real*8 (a-h,o-z) include 'DIMENSIONS' - include 'sizesclu.dat' include 'COMMON.IOUNITS' -#ifdef MPL - include 'COMMON.INFO' +#ifdef MPI + include "mpif.h" #endif include 'COMMON.FFIELD' include 'COMMON.DERIV' + include 'COMMON.LOCAL' include 'COMMON.INTERACT' include 'COMMON.CONTACTS' -#ifdef MPL - parameter (max_cont=maxconts) - parameter (max_dim=2*(8*3+2)) - parameter (msglen1=max_cont*max_dim*4) - parameter (msglen2=2*msglen1) - integer source,CorrelType,CorrelID,Error - double precision buffer(max_cont,max_dim) -#endif + include 'COMMON.CHAIN' + include 'COMMON.CONTROL' + include 'COMMON.SHIELD' double precision gx(3),gx1(3) + integer num_cont_hb_old(maxres) logical lprn,ldone - + double precision eello4,eello5,eelo6,eello_turn6 + external eello4,eello5,eello6,eello_turn6 C Set lprn=.true. for debugging lprn=.false. eturn6=0.0d0 -#ifdef MPL - n_corr=0 - n_corr1=0 - if (fgProcs.le.1) goto 30 if (lprn) then write (iout,'(a)') 'Contact function values:' do i=nnt,nct-2 - write (iout,'(2i3,50(1x,i2,f5.2))') - & i,num_cont_hb(i),(jcont_hb(j,i),facont_hb(j,i), - & j=1,num_cont_hb(i)) - enddo - endif -C Caution! Following code assumes that electrostatic interactions concerning -C a given atom are split among at most two processors! - CorrelType=477 - CorrelID=MyID+1 - ldone=.false. - do i=1,max_cont - do j=1,max_dim - buffer(i,j)=0.0D0 - enddo - enddo - mm=mod(MyRank,2) -cd write (iout,*) 'MyRank',MyRank,' mm',mm - if (mm) 20,20,10 - 10 continue -cd write (iout,*) 'Sending: MyRank',MyRank,' mm',mm,' ldone',ldone - if (MyRank.gt.0) then -C Send correlation contributions to the preceding processor - msglen=msglen1 - nn=num_cont_hb(iatel_s) - call pack_buffer(max_cont,max_dim,iatel_s,0,buffer) -cd write (iout,*) 'The BUFFER array:' -cd do i=1,nn -cd write (iout,'(i2,9(3f8.3,2x))') i,(buffer(i,j),j=1,26) -cd enddo - if (ielstart(iatel_s).gt.iatel_s+ispp) then - msglen=msglen2 - call pack_buffer(max_cont,max_dim,iatel_s+1,26,buffer) -C Clear the contacts of the atom passed to the neighboring processor - nn=num_cont_hb(iatel_s+1) -cd do i=1,nn -cd write (iout,'(i2,9(3f8.3,2x))') i,(buffer(i,j+26),j=1,26) -cd enddo - num_cont_hb(iatel_s)=0 - endif -cd write (iout,*) 'Processor ',MyID,MyRank, -cd & ' is sending correlation contribution to processor',MyID-1, -cd & ' msglen=',msglen -cd write (*,*) 'Processor ',MyID,MyRank, -cd & ' is sending correlation contribution to processor',MyID-1, -cd & ' msglen=',msglen,' CorrelType=',CorrelType - call mp_bsend(buffer,msglen,MyID-1,CorrelType,CorrelID) -cd write (iout,*) 'Processor ',MyID, -cd & ' has sent correlation contribution to processor',MyID-1, -cd & ' msglen=',msglen,' CorrelID=',CorrelID -cd write (*,*) 'Processor ',MyID, -cd & ' has sent correlation contribution to processor',MyID-1, -cd & ' msglen=',msglen,' CorrelID=',CorrelID - msglen=msglen1 - endif ! (MyRank.gt.0) - if (ldone) goto 30 - ldone=.true. - 20 continue -cd write (iout,*) 'Receiving: MyRank',MyRank,' mm',mm,' ldone',ldone - if (MyRank.lt.fgProcs-1) then -C Receive correlation contributions from the next processor - msglen=msglen1 - if (ielend(iatel_e).lt.nct-1) msglen=msglen2 -cd write (iout,*) 'Processor',MyID, -cd & ' is receiving correlation contribution from processor',MyID+1, -cd & ' msglen=',msglen,' CorrelType=',CorrelType -cd write (*,*) 'Processor',MyID, -cd & ' is receiving correlation contribution from processor',MyID+1, -cd & ' msglen=',msglen,' CorrelType=',CorrelType - nbytes=-1 - do while (nbytes.le.0) - call mp_probe(MyID+1,CorrelType,nbytes) - enddo -cd print *,'Processor',MyID,' msglen',msglen,' nbytes',nbytes - call mp_brecv(buffer,msglen,MyID+1,CorrelType,nbytes) -cd write (iout,*) 'Processor',MyID, -cd & ' has received correlation contribution from processor',MyID+1, -cd & ' msglen=',msglen,' nbytes=',nbytes -cd write (iout,*) 'The received BUFFER array:' -cd do i=1,max_cont -cd write (iout,'(i2,9(3f8.3,2x))') i,(buffer(i,j),j=1,52) -cd enddo - if (msglen.eq.msglen1) then - call unpack_buffer(max_cont,max_dim,iatel_e+1,0,buffer) - else if (msglen.eq.msglen2) then - call unpack_buffer(max_cont,max_dim,iatel_e,0,buffer) - call unpack_buffer(max_cont,max_dim,iatel_e+1,26,buffer) - else - write (iout,*) - & 'ERROR!!!! message length changed while processing correlations.' - write (*,*) - & 'ERROR!!!! message length changed while processing correlations.' - call mp_stopall(Error) - endif ! msglen.eq.msglen1 - endif ! MyRank.lt.fgProcs-1 - if (ldone) goto 30 - ldone=.true. - goto 10 - 30 continue -#endif - if (lprn) then - write (iout,'(a)') 'Contact function values:' - do i=nnt,nct-2 - write (iout,'(2i3,50(1x,i2,f5.2))') - & i,num_cont_hb(i),(jcont_hb(j,i),facont_hb(j,i), - & j=1,num_cont_hb(i)) + write (iout,'(2i3,50(1x,i2,5f6.3))') + & i,num_cont_hb(i),(jcont_hb(j,i),d_cont(j,i), + & ((a_chuj(ll,kk,j,i),ll=1,2),kk=1,2),j=1,num_cont_hb(i)) enddo endif ecorr=0.0D0 @@ -5001,22 +6445,35 @@ C Calculate the dipole-dipole interaction energies num_conti=num_cont_hb(i) do jj=1,num_conti j=jcont_hb(jj,i) +#ifdef MOMENT call dipole(i,j,jj) +#endif enddo enddo endif C Calculate the local-electrostatic correlation terms - do i=iatel_s,iatel_e+1 +c write (iout,*) "gradcorr5 in eello5 before loop" +c do iii=1,nres +c write (iout,'(i5,3f10.5)') +c & iii,(gradcorr5(jjj,iii),jjj=1,3) +c enddo + do i=min0(iatel_s,iturn4_start),max0(iatel_e+1,iturn3_end+1) +c write (iout,*) "corr loop i",i i1=i+1 num_conti=num_cont_hb(i) num_conti1=num_cont_hb(i+1) do jj=1,num_conti j=jcont_hb(jj,i) + jp=iabs(j) do kk=1,num_conti1 j1=jcont_hb(kk,i1) -c write (*,*) 'i=',i,' j=',j,' i1=',i1,' j1=',j1, + jp1=iabs(j1) +c write (iout,*) 'i=',i,' j=',j,' i1=',i1,' j1=',j1, c & ' jj=',jj,' kk=',kk - if (j1.eq.j+1 .or. j1.eq.j-1) then +c if (j1.eq.j+1 .or. j1.eq.j-1) then + if ((j.gt.0 .and. j1.gt.0 .or. j.gt.0 .and. j1.lt.0 + & .or. j.lt.0 .and. j1.gt.0) .and. + & (jp1.eq.jp+1 .or. jp1.eq.jp-1)) then C Contacts I-J and (I+1)-(J+1) or (I+1)-(J-1) occur simultaneously. C The system gains extra energy. n_corr=n_corr+1 @@ -5026,8 +6483,8 @@ C The system gains extra energy. IF (sred_geom.lt.cutoff_corr) THEN call gcont(sred_geom,r0_corr,1.0D0,delt_corr, & ekont,fprimcont) -c write (*,*) 'i=',i,' j=',j,' i1=',i1,' j1=',j1, -c & ' jj=',jj,' kk=',kk +cd write (iout,*) 'i=',i,' j=',jp,' i1=',i1,' j1=',jp1, +cd & ' jj=',jj,' kk=',kk fac_prim1=0.5d0*sqd2/sqd1*fprimcont fac_prim2=0.5d0*sqd1/sqd2*fprimcont do l=1,3 @@ -5036,51 +6493,69 @@ c & ' jj=',jj,' kk=',kk enddo n_corr1=n_corr1+1 cd write (iout,*) 'sred_geom=',sred_geom, -cd & ' ekont=',ekont,' fprim=',fprimcont - call calc_eello(i,j,i+1,j1,jj,kk) +cd & ' ekont=',ekont,' fprim=',fprimcont, +cd & ' fac_prim1',fac_prim1,' fac_prim2',fac_prim2 +cd write (iout,*) "g_contij",g_contij +cd write (iout,*) "grij_hb_cont i",grij_hb_cont(:,jj,i) +cd write (iout,*) "grij_hb_cont i1",grij_hb_cont(:,jj,i1) + call calc_eello(i,jp,i+1,jp1,jj,kk) if (wcorr4.gt.0.0d0) - & ecorr=ecorr+eello4(i,j,i+1,j1,jj,kk) + & ecorr=ecorr+eello4(i,jp,i+1,jp1,jj,kk) +CC & *fac_shield(i)**2*fac_shield(j)**2 + if (energy_dec.and.wcorr4.gt.0.0d0) + 1 write (iout,'(a6,4i5,0pf7.3)') + 2 'ecorr4',i,j,i+1,j1,eello4(i,jp,i+1,jp1,jj,kk) +c write (iout,*) "gradcorr5 before eello5" +c do iii=1,nres +c write (iout,'(i5,3f10.5)') +c & iii,(gradcorr5(jjj,iii),jjj=1,3) +c enddo if (wcorr5.gt.0.0d0) - & ecorr5=ecorr5+eello5(i,j,i+1,j1,jj,kk) -c print *,"wcorr5",ecorr5 + & ecorr5=ecorr5+eello5(i,jp,i+1,jp1,jj,kk) +c write (iout,*) "gradcorr5 after eello5" +c do iii=1,nres +c write (iout,'(i5,3f10.5)') +c & iii,(gradcorr5(jjj,iii),jjj=1,3) +c enddo + if (energy_dec.and.wcorr5.gt.0.0d0) + 1 write (iout,'(a6,4i5,0pf7.3)') + 2 'ecorr5',i,j,i+1,j1,eello5(i,jp,i+1,jp1,jj,kk) cd write(2,*)'wcorr6',wcorr6,' wturn6',wturn6 -cd write(2,*)'ijkl',i,j,i+1,j1 - if (wcorr6.gt.0.0d0 .and. (j.ne.i+4 .or. j1.ne.i+3 +cd write(2,*)'ijkl',i,jp,i+1,jp1 + if (wcorr6.gt.0.0d0 .and. (jp.ne.i+4 .or. jp1.ne.i+3 & .or. wturn6.eq.0.0d0))then cd write (iout,*) '******ecorr6: i,j,i+1,j1',i,j,i+1,j1 - ecorr6=ecorr6+eello6(i,j,i+1,j1,jj,kk) + ecorr6=ecorr6+eello6(i,jp,i+1,jp1,jj,kk) + if (energy_dec) write (iout,'(a6,4i5,0pf7.3)') + 1 'ecorr6',i,j,i+1,j1,eello6(i,jp,i+1,jp1,jj,kk) cd write (iout,*) 'ecorr',ecorr,' ecorr5=',ecorr5, cd & 'ecorr6=',ecorr6 cd write (iout,'(4e15.5)') sred_geom, -cd & dabs(eello4(i,j,i+1,j1,jj,kk)), -cd & dabs(eello5(i,j,i+1,j1,jj,kk)), -cd & dabs(eello6(i,j,i+1,j1,jj,kk)) +cd & dabs(eello4(i,jp,i+1,jp1,jj,kk)), +cd & dabs(eello5(i,jp,i+1,jp1,jj,kk)), +cd & dabs(eello6(i,jp,i+1,jp1,jj,kk)) else if (wturn6.gt.0.0d0 - & .and. (j.eq.i+4 .and. j1.eq.i+3)) then -cd write (iout,*) '******eturn6: i,j,i+1,j1',i,j,i+1,j1 + & .and. (jp.eq.i+4 .and. jp1.eq.i+3)) then +cd write (iout,*) '******eturn6: i,j,i+1,j1',i,jip,i+1,jp1 eturn6=eturn6+eello_turn6(i,jj,kk) + if (energy_dec) write (iout,'(a6,4i5,0pf7.3)') + 1 'eturn6',i,j,i+1,j1,eello_turn6(i,jj,kk) cd write (2,*) 'multibody_eello:eturn6',eturn6 - endif - ENDIF -1111 continue - else if (j1.eq.j) then -C Contacts I-J and I-(J+1) occur simultaneously. -C The system loses extra energy. -c ecorr=ecorr+ehbcorr(i,j,i+1,j,jj,kk,0.60D0,-0.40D0) + endif + ENDIF +1111 continue endif enddo ! kk - do kk=1,num_conti - j1=jcont_hb(kk,i) -c write (iout,*) 'i=',i,' j=',j,' i1=',i1,' j1=',j1, -c & ' jj=',jj,' kk=',kk - if (j1.eq.j+1) then -C Contacts I-J and (I+1)-J occur simultaneously. -C The system loses extra energy. -c ecorr=ecorr+ehbcorr(i,j,i,j+1,jj,kk,0.60D0,-0.40D0) - endif ! j1==j+1 - enddo ! kk enddo ! jj enddo ! i + do i=1,nres + num_cont_hb(i)=num_cont_hb_old(i) + enddo +c write (iout,*) "gradcorr5 in eello5" +c do iii=1,nres +c write (iout,'(i5,3f10.5)') +c & iii,(gradcorr5(jjj,iii),jjj=1,3) +c enddo return end c------------------------------------------------------------------------------ @@ -5091,9 +6566,12 @@ c------------------------------------------------------------------------------ include 'COMMON.DERIV' include 'COMMON.INTERACT' include 'COMMON.CONTACTS' + include 'COMMON.SHIELD' + include 'COMMON.CONTROL' double precision gx(3),gx1(3) logical lprn lprn=.false. +C print *,"wchodze",fac_shield(i),shield_mode eij=facont_hb(jj,i) ekl=facont_hb(kk,k) ees0pij=ees0p(jj,i) @@ -5102,62 +6580,161 @@ c------------------------------------------------------------------------------ ees0mkl=ees0m(kk,k) ekont=eij*ekl ees=-(coeffp*ees0pij*ees0pkl+coeffm*ees0mij*ees0mkl) +C* +C & fac_shield(i)**2*fac_shield(j)**2 cd ees=-(coeffp*ees0pkl+coeffm*ees0mkl) C Following 4 lines for diagnostics. cd ees0pkl=0.0D0 cd ees0pij=1.0D0 cd ees0mkl=0.0D0 cd ees0mij=1.0D0 -c write (iout,*)'Contacts have occurred for peptide groups',i,j, -c & ' and',k,l -c write (iout,*)'Contacts have occurred for peptide groups', -c & i,j,' fcont:',eij,' eij',' eesij',ees0pij,ees0mij,' and ',k,l -c & ,' fcont ',ekl,' eeskl',ees0pkl,ees0mkl,' ees=',ees +c write (iout,'(2(a,2i3,a,f10.5,a,2f10.5),a,f10.5,a,$)') +c & 'Contacts ',i,j, +c & ' eij',eij,' eesij',ees0pij,ees0mij,' and ',k,l +c & ,' fcont ',ekl,' eeskl',ees0pkl,ees0mkl,' energy=',ekont*ees, +c & 'gradcorr_long' C Calculate the multi-body contribution to energy. - ecorr=ecorr+ekont*ees - if (calc_grad) then +C ecorr=ecorr+ekont*ees C Calculate multi-body contributions to the gradient. + coeffpees0pij=coeffp*ees0pij + coeffmees0mij=coeffm*ees0mij + coeffpees0pkl=coeffp*ees0pkl + coeffmees0mkl=coeffm*ees0mkl do ll=1,3 - ghalf=0.5D0*ees*ekl*gacont_hbr(ll,jj,i) - gradcorr(ll,i)=gradcorr(ll,i)+ghalf - & -ekont*(coeffp*ees0pkl*gacontp_hb1(ll,jj,i)+ - & coeffm*ees0mkl*gacontm_hb1(ll,jj,i)) - gradcorr(ll,j)=gradcorr(ll,j)+ghalf - & -ekont*(coeffp*ees0pkl*gacontp_hb2(ll,jj,i)+ - & coeffm*ees0mkl*gacontm_hb2(ll,jj,i)) - ghalf=0.5D0*ees*eij*gacont_hbr(ll,kk,k) - gradcorr(ll,k)=gradcorr(ll,k)+ghalf - & -ekont*(coeffp*ees0pij*gacontp_hb1(ll,kk,k)+ - & coeffm*ees0mij*gacontm_hb1(ll,kk,k)) - gradcorr(ll,l)=gradcorr(ll,l)+ghalf - & -ekont*(coeffp*ees0pij*gacontp_hb2(ll,kk,k)+ - & coeffm*ees0mij*gacontm_hb2(ll,kk,k)) - enddo - do m=i+1,j-1 - do ll=1,3 - gradcorr(ll,m)=gradcorr(ll,m)+ - & ees*ekl*gacont_hbr(ll,jj,i)- - & ekont*(coeffp*ees0pkl*gacontp_hb3(ll,jj,i)+ - & coeffm*ees0mkl*gacontm_hb3(ll,jj,i)) - enddo +cgrad ghalfi=ees*ekl*gacont_hbr(ll,jj,i) + gradcorr(ll,i)=gradcorr(ll,i)!+0.5d0*ghalfi + & -ekont*(coeffpees0pkl*gacontp_hb1(ll,jj,i)+ + & coeffmees0mkl*gacontm_hb1(ll,jj,i)) + gradcorr(ll,j)=gradcorr(ll,j)!+0.5d0*ghalfi + & -ekont*(coeffpees0pkl*gacontp_hb2(ll,jj,i)+ + & coeffmees0mkl*gacontm_hb2(ll,jj,i)) +cgrad ghalfk=ees*eij*gacont_hbr(ll,kk,k) + gradcorr(ll,k)=gradcorr(ll,k)!+0.5d0*ghalfk + & -ekont*(coeffpees0pij*gacontp_hb1(ll,kk,k)+ + & coeffmees0mij*gacontm_hb1(ll,kk,k)) + gradcorr(ll,l)=gradcorr(ll,l)!+0.5d0*ghalfk + & -ekont*(coeffpees0pij*gacontp_hb2(ll,kk,k)+ + & coeffmees0mij*gacontm_hb2(ll,kk,k)) + gradlongij=ees*ekl*gacont_hbr(ll,jj,i)- + & ekont*(coeffpees0pkl*gacontp_hb3(ll,jj,i)+ + & coeffmees0mkl*gacontm_hb3(ll,jj,i)) + gradcorr_long(ll,j)=gradcorr_long(ll,j)+gradlongij + gradcorr_long(ll,i)=gradcorr_long(ll,i)-gradlongij + gradlongkl=ees*eij*gacont_hbr(ll,kk,k)- + & ekont*(coeffpees0pij*gacontp_hb3(ll,kk,k)+ + & coeffmees0mij*gacontm_hb3(ll,kk,k)) + gradcorr_long(ll,l)=gradcorr_long(ll,l)+gradlongkl + gradcorr_long(ll,k)=gradcorr_long(ll,k)-gradlongkl +c write (iout,'(2f10.5,2x,$)') gradlongij,gradlongkl enddo - do m=k+1,l-1 - do ll=1,3 - gradcorr(ll,m)=gradcorr(ll,m)+ - & ees*eij*gacont_hbr(ll,kk,k)- - & ekont*(coeffp*ees0pij*gacontp_hb3(ll,kk,k)+ - & coeffm*ees0mij*gacontm_hb3(ll,kk,k)) - enddo - enddo - endif +c write (iout,*) +cgrad do m=i+1,j-1 +cgrad do ll=1,3 +cgrad gradcorr(ll,m)=gradcorr(ll,m)+ +cgrad & ees*ekl*gacont_hbr(ll,jj,i)- +cgrad & ekont*(coeffp*ees0pkl*gacontp_hb3(ll,jj,i)+ +cgrad & coeffm*ees0mkl*gacontm_hb3(ll,jj,i)) +cgrad enddo +cgrad enddo +cgrad do m=k+1,l-1 +cgrad do ll=1,3 +cgrad gradcorr(ll,m)=gradcorr(ll,m)+ +cgrad & ees*eij*gacont_hbr(ll,kk,k)- +cgrad & ekont*(coeffp*ees0pij*gacontp_hb3(ll,kk,k)+ +cgrad & coeffm*ees0mij*gacontm_hb3(ll,kk,k)) +cgrad enddo +cgrad enddo +c write (iout,*) "ehbcorr",ekont*ees +C print *,ekont,ees,i,k ehbcorr=ekont*ees +C now gradient over shielding +C return + if (shield_mode.gt.0) then + j=ees0plist(jj,i) + l=ees0plist(kk,k) +C print *,i,j,fac_shield(i),fac_shield(j), +C &fac_shield(k),fac_shield(l) + if ((fac_shield(i).gt.0).and.(fac_shield(j).gt.0).and. + & (fac_shield(k).gt.0).and.(fac_shield(l).gt.0)) then + do ilist=1,ishield_list(i) + iresshield=shield_list(ilist,i) + do m=1,3 + rlocshield=grad_shield_side(m,ilist,i)*ehbcorr/fac_shield(i) +C & *2.0 + gshieldx_ec(m,iresshield)=gshieldx_ec(m,iresshield)+ + & rlocshield + & +grad_shield_loc(m,ilist,i)*ehbcorr/fac_shield(i) + gshieldc_ec(m,iresshield-1)=gshieldc_ec(m,iresshield-1) + &+rlocshield + enddo + enddo + do ilist=1,ishield_list(j) + iresshield=shield_list(ilist,j) + do m=1,3 + rlocshield=grad_shield_side(m,ilist,j)*ehbcorr/fac_shield(j) +C & *2.0 + gshieldx_ec(m,iresshield)=gshieldx_ec(m,iresshield)+ + & rlocshield + & +grad_shield_loc(m,ilist,j)*ehbcorr/fac_shield(j) + gshieldc_ec(m,iresshield-1)=gshieldc_ec(m,iresshield-1) + & +rlocshield + enddo + enddo + + do ilist=1,ishield_list(k) + iresshield=shield_list(ilist,k) + do m=1,3 + rlocshield=grad_shield_side(m,ilist,k)*ehbcorr/fac_shield(k) +C & *2.0 + gshieldx_ec(m,iresshield)=gshieldx_ec(m,iresshield)+ + & rlocshield + & +grad_shield_loc(m,ilist,k)*ehbcorr/fac_shield(k) + gshieldc_ec(m,iresshield-1)=gshieldc_ec(m,iresshield-1) + & +rlocshield + enddo + enddo + do ilist=1,ishield_list(l) + iresshield=shield_list(ilist,l) + do m=1,3 + rlocshield=grad_shield_side(m,ilist,l)*ehbcorr/fac_shield(l) +C & *2.0 + gshieldx_ec(m,iresshield)=gshieldx_ec(m,iresshield)+ + & rlocshield + & +grad_shield_loc(m,ilist,l)*ehbcorr/fac_shield(l) + gshieldc_ec(m,iresshield-1)=gshieldc_ec(m,iresshield-1) + & +rlocshield + enddo + enddo +C print *,gshieldx(m,iresshield) + do m=1,3 + gshieldc_ec(m,i)=gshieldc_ec(m,i)+ + & grad_shield(m,i)*ehbcorr/fac_shield(i) + gshieldc_ec(m,j)=gshieldc_ec(m,j)+ + & grad_shield(m,j)*ehbcorr/fac_shield(j) + gshieldc_ec(m,i-1)=gshieldc_ec(m,i-1)+ + & grad_shield(m,i)*ehbcorr/fac_shield(i) + gshieldc_ec(m,j-1)=gshieldc_ec(m,j-1)+ + & grad_shield(m,j)*ehbcorr/fac_shield(j) + + gshieldc_ec(m,k)=gshieldc_ec(m,k)+ + & grad_shield(m,k)*ehbcorr/fac_shield(k) + gshieldc_ec(m,l)=gshieldc_ec(m,l)+ + & grad_shield(m,l)*ehbcorr/fac_shield(l) + gshieldc_ec(m,k-1)=gshieldc_ec(m,k-1)+ + & grad_shield(m,k)*ehbcorr/fac_shield(k) + gshieldc_ec(m,l-1)=gshieldc_ec(m,l-1)+ + & grad_shield(m,l)*ehbcorr/fac_shield(l) + + enddo + endif + endif return end +#ifdef MOMENT C--------------------------------------------------------------------------- subroutine dipole(i,j,jj) implicit real*8 (a-h,o-z) include 'DIMENSIONS' - include 'sizesclu.dat' include 'COMMON.IOUNITS' include 'COMMON.CHAIN' include 'COMMON.FFIELD' @@ -5171,17 +6748,17 @@ C--------------------------------------------------------------------------- & auxmat(2,2) iti1 = itortyp(itype(i+1)) if (j.lt.nres-1) then - itj1 = itortyp(itype(j+1)) + itj1 = itype2loc(itype(j+1)) else - itj1=ntortyp+1 + itj1=nloctyp endif do iii=1,2 dipi(iii,1)=Ub2(iii,i) dipderi(iii)=Ub2der(iii,i) - dipi(iii,2)=b1(iii,iti1) + dipi(iii,2)=b1(iii,i+1) dipj(iii,1)=Ub2(iii,j) dipderj(iii)=Ub2der(iii,j) - dipj(iii,2)=b1(iii,itj1) + dipj(iii,2)=b1(iii,j+1) enddo kkk=0 do iii=1,2 @@ -5191,7 +6768,6 @@ C--------------------------------------------------------------------------- dip(kkk,jj,i)=scalar2(dipi(1,jjj),auxvec(1)) enddo enddo - if (.not.calc_grad) return do kkk=1,5 do lll=1,3 mmm=0 @@ -5216,6 +6792,7 @@ C--------------------------------------------------------------------------- enddo return end +#endif C--------------------------------------------------------------------------- subroutine calc_eello(i,j,k,l,jj,kk) C @@ -5224,7 +6801,6 @@ C the fourth-, fifth-, and sixth-order local-electrostatic terms. C implicit real*8 (a-h,o-z) include 'DIMENSIONS' - include 'sizesclu.dat' include 'COMMON.IOUNITS' include 'COMMON.CHAIN' include 'COMMON.DERIV' @@ -5241,6 +6817,8 @@ C cd write (iout,*) 'calc_eello: i=',i,' j=',j,' k=',k,' l=',l, cd & ' jj=',jj,' kk=',kk cd if (i.ne.2 .or. j.ne.4 .or. k.ne.3 .or. l.ne.5) return +cd write (iout,*) "a_chujij",((a_chuj(iii,jjj,jj,i),iii=1,2),jjj=1,2) +cd write (iout,*) "a_chujkl",((a_chuj(iii,jjj,kk,k),iii=1,2),jjj=1,2) do iii=1,2 do jjj=1,2 aa1(iii,jjj)=a_chuj(iii,jjj,jj,i) @@ -5260,16 +6838,16 @@ cd if (i.ne.2 .or. j.ne.4 .or. k.ne.3 .or. l.ne.5) return if (l.eq.j+1) then C parallel orientation of the two CA-CA-CA frames. if (i.gt.1) then - iti=itortyp(itype(i)) + iti=itype2loc(itype(i)) else - iti=ntortyp+1 + iti=nloctyp endif - itk1=itortyp(itype(k+1)) - itj=itortyp(itype(j)) + itk1=itype2loc(itype(k+1)) + itj=itype2loc(itype(j)) if (l.lt.nres-1) then - itl1=itortyp(itype(l+1)) + itl1=itype2loc(itype(l+1)) else - itl1=ntortyp+1 + itl1=nloctyp endif C A1 kernel(j+1) A2T cd do iii=1,2 @@ -5360,26 +6938,26 @@ C They are needed only when the fifth- or the sixth-order cumulants are C indluded. IF (wcorr5.gt.0.0d0 .or. wcorr6.gt.0.0d0) THEN call transpose2(AEA(1,1,1),auxmat(1,1)) - call matvec2(auxmat(1,1),b1(1,iti),AEAb1(1,1,1)) + call matvec2(auxmat(1,1),b1(1,i),AEAb1(1,1,1)) call matvec2(auxmat(1,1),Ub2(1,i),AEAb2(1,1,1)) call matvec2(auxmat(1,1),Ub2der(1,i),AEAb2derg(1,2,1,1)) call transpose2(AEAderg(1,1,1),auxmat(1,1)) - call matvec2(auxmat(1,1),b1(1,iti),AEAb1derg(1,1,1)) + call matvec2(auxmat(1,1),b1(1,i),AEAb1derg(1,1,1)) call matvec2(auxmat(1,1),Ub2(1,i),AEAb2derg(1,1,1,1)) - call matvec2(AEA(1,1,1),b1(1,itk1),AEAb1(1,2,1)) - call matvec2(AEAderg(1,1,1),b1(1,itk1),AEAb1derg(1,2,1)) + call matvec2(AEA(1,1,1),b1(1,k+1),AEAb1(1,2,1)) + call matvec2(AEAderg(1,1,1),b1(1,k+1),AEAb1derg(1,2,1)) call matvec2(AEA(1,1,1),Ub2(1,k+1),AEAb2(1,2,1)) call matvec2(AEAderg(1,1,1),Ub2(1,k+1),AEAb2derg(1,1,2,1)) call matvec2(AEA(1,1,1),Ub2der(1,k+1),AEAb2derg(1,2,2,1)) call transpose2(AEA(1,1,2),auxmat(1,1)) - call matvec2(auxmat(1,1),b1(1,itj),AEAb1(1,1,2)) + call matvec2(auxmat(1,1),b1(1,j),AEAb1(1,1,2)) call matvec2(auxmat(1,1),Ub2(1,j),AEAb2(1,1,2)) call matvec2(auxmat(1,1),Ub2der(1,j),AEAb2derg(1,2,1,2)) call transpose2(AEAderg(1,1,2),auxmat(1,1)) - call matvec2(auxmat(1,1),b1(1,itj),AEAb1derg(1,1,2)) + call matvec2(auxmat(1,1),b1(1,j),AEAb1derg(1,1,2)) call matvec2(auxmat(1,1),Ub2(1,j),AEAb2derg(1,1,1,2)) - call matvec2(AEA(1,1,2),b1(1,itl1),AEAb1(1,2,2)) - call matvec2(AEAderg(1,1,2),b1(1,itl1),AEAb1derg(1,2,2)) + call matvec2(AEA(1,1,2),b1(1,l+1),AEAb1(1,2,2)) + call matvec2(AEAderg(1,1,2),b1(1,l+1),AEAb1derg(1,2,2)) call matvec2(AEA(1,1,2),Ub2(1,l+1),AEAb2(1,2,2)) call matvec2(AEAderg(1,1,2),Ub2(1,l+1),AEAb2derg(1,1,2,2)) call matvec2(AEA(1,1,2),Ub2der(1,l+1),AEAb2derg(1,2,2,2)) @@ -5388,20 +6966,20 @@ C Calculate the Cartesian derivatives of the vectors. do kkk=1,5 do lll=1,3 call transpose2(AEAderx(1,1,lll,kkk,iii,1),auxmat(1,1)) - call matvec2(auxmat(1,1),b1(1,iti), + call matvec2(auxmat(1,1),b1(1,i), & AEAb1derx(1,lll,kkk,iii,1,1)) call matvec2(auxmat(1,1),Ub2(1,i), & AEAb2derx(1,lll,kkk,iii,1,1)) - call matvec2(AEAderx(1,1,lll,kkk,iii,1),b1(1,itk1), + call matvec2(AEAderx(1,1,lll,kkk,iii,1),b1(1,k+1), & AEAb1derx(1,lll,kkk,iii,2,1)) call matvec2(AEAderx(1,1,lll,kkk,iii,1),Ub2(1,k+1), & AEAb2derx(1,lll,kkk,iii,2,1)) call transpose2(AEAderx(1,1,lll,kkk,iii,2),auxmat(1,1)) - call matvec2(auxmat(1,1),b1(1,itj), + call matvec2(auxmat(1,1),b1(1,j), & AEAb1derx(1,lll,kkk,iii,1,2)) call matvec2(auxmat(1,1),Ub2(1,j), & AEAb2derx(1,lll,kkk,iii,1,2)) - call matvec2(AEAderx(1,1,lll,kkk,iii,2),b1(1,itl1), + call matvec2(AEAderx(1,1,lll,kkk,iii,2),b1(1,l+1), & AEAb1derx(1,lll,kkk,iii,2,2)) call matvec2(AEAderx(1,1,lll,kkk,iii,2),Ub2(1,l+1), & AEAb2derx(1,lll,kkk,iii,2,2)) @@ -5413,17 +6991,17 @@ C End vectors else C Antiparallel orientation of the two CA-CA-CA frames. if (i.gt.1) then - iti=itortyp(itype(i)) + iti=itype2loc(itype(i)) else - iti=ntortyp+1 + iti=nloctyp endif - itk1=itortyp(itype(k+1)) - itl=itortyp(itype(l)) - itj=itortyp(itype(j)) + itk1=itype2loc(itype(k+1)) + itl=itype2loc(itype(l)) + itj=itype2loc(itype(j)) if (j.lt.nres-1) then - itj1=itortyp(itype(j+1)) + itj1=itype2loc(itype(j+1)) else - itj1=ntortyp+1 + itj1=nloctyp 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), @@ -5498,26 +7076,26 @@ C indluded. IF (wcorr5.gt.0.0d0 .or. wcorr6.gt.0.0d0 .or. & (wturn6.gt.0.0d0 .and. j.eq.i+4 .and. l.eq.i+3)) THEN call transpose2(AEA(1,1,1),auxmat(1,1)) - call matvec2(auxmat(1,1),b1(1,iti),AEAb1(1,1,1)) + call matvec2(auxmat(1,1),b1(1,i),AEAb1(1,1,1)) call matvec2(auxmat(1,1),Ub2(1,i),AEAb2(1,1,1)) call matvec2(auxmat(1,1),Ub2der(1,i),AEAb2derg(1,2,1,1)) call transpose2(AEAderg(1,1,1),auxmat(1,1)) - call matvec2(auxmat(1,1),b1(1,iti),AEAb1derg(1,1,1)) + call matvec2(auxmat(1,1),b1(1,i),AEAb1derg(1,1,1)) call matvec2(auxmat(1,1),Ub2(1,i),AEAb2derg(1,1,1,1)) - call matvec2(AEA(1,1,1),b1(1,itk1),AEAb1(1,2,1)) - call matvec2(AEAderg(1,1,1),b1(1,itk1),AEAb1derg(1,2,1)) + call matvec2(AEA(1,1,1),b1(1,k+1),AEAb1(1,2,1)) + call matvec2(AEAderg(1,1,1),b1(1,k+1),AEAb1derg(1,2,1)) call matvec2(AEA(1,1,1),Ub2(1,k+1),AEAb2(1,2,1)) call matvec2(AEAderg(1,1,1),Ub2(1,k+1),AEAb2derg(1,1,2,1)) call matvec2(AEA(1,1,1),Ub2der(1,k+1),AEAb2derg(1,2,2,1)) call transpose2(AEA(1,1,2),auxmat(1,1)) - call matvec2(auxmat(1,1),b1(1,itj1),AEAb1(1,1,2)) + call matvec2(auxmat(1,1),b1(1,j+1),AEAb1(1,1,2)) call matvec2(auxmat(1,1),Ub2(1,l),AEAb2(1,1,2)) call matvec2(auxmat(1,1),Ub2der(1,l),AEAb2derg(1,2,1,2)) call transpose2(AEAderg(1,1,2),auxmat(1,1)) - call matvec2(auxmat(1,1),b1(1,itl),AEAb1(1,1,2)) + call matvec2(auxmat(1,1),b1(1,l),AEAb1(1,1,2)) call matvec2(auxmat(1,1),Ub2(1,l),AEAb2derg(1,1,1,2)) - call matvec2(AEA(1,1,2),b1(1,itj1),AEAb1(1,2,2)) - call matvec2(AEAderg(1,1,2),b1(1,itj1),AEAb1derg(1,2,2)) + call matvec2(AEA(1,1,2),b1(1,j+1),AEAb1(1,2,2)) + call matvec2(AEAderg(1,1,2),b1(1,j+1),AEAb1derg(1,2,2)) call matvec2(AEA(1,1,2),Ub2(1,j),AEAb2(1,2,2)) call matvec2(AEAderg(1,1,2),Ub2(1,j),AEAb2derg(1,1,2,2)) call matvec2(AEA(1,1,2),Ub2der(1,j),AEAb2derg(1,2,2,2)) @@ -5526,20 +7104,20 @@ C Calculate the Cartesian derivatives of the vectors. do kkk=1,5 do lll=1,3 call transpose2(AEAderx(1,1,lll,kkk,iii,1),auxmat(1,1)) - call matvec2(auxmat(1,1),b1(1,iti), + call matvec2(auxmat(1,1),b1(1,i), & AEAb1derx(1,lll,kkk,iii,1,1)) call matvec2(auxmat(1,1),Ub2(1,i), & AEAb2derx(1,lll,kkk,iii,1,1)) - call matvec2(AEAderx(1,1,lll,kkk,iii,1),b1(1,itk1), + call matvec2(AEAderx(1,1,lll,kkk,iii,1),b1(1,k+1), & AEAb1derx(1,lll,kkk,iii,2,1)) call matvec2(AEAderx(1,1,lll,kkk,iii,1),Ub2(1,k+1), & AEAb2derx(1,lll,kkk,iii,2,1)) call transpose2(AEAderx(1,1,lll,kkk,iii,2),auxmat(1,1)) - call matvec2(auxmat(1,1),b1(1,itl), + call matvec2(auxmat(1,1),b1(1,l), & AEAb1derx(1,lll,kkk,iii,1,2)) call matvec2(auxmat(1,1),Ub2(1,l), & AEAb2derx(1,lll,kkk,iii,1,2)) - call matvec2(AEAderx(1,1,lll,kkk,iii,2),b1(1,itj1), + call matvec2(AEAderx(1,1,lll,kkk,iii,2),b1(1,j+1), & AEAb1derx(1,lll,kkk,iii,2,2)) call matvec2(AEAderx(1,1,lll,kkk,iii,2),Ub2(1,j), & AEAb2derx(1,lll,kkk,iii,2,2)) @@ -5601,7 +7179,6 @@ C--------------------------------------------------------------------------- double precision function eello4(i,j,k,l,jj,kk) implicit real*8 (a-h,o-z) include 'DIMENSIONS' - include 'sizesclu.dat' include 'COMMON.IOUNITS' include 'COMMON.CHAIN' include 'COMMON.DERIV' @@ -5664,51 +7241,49 @@ cd & ' fcont ',ekl,' eel4=',eel4,' eel4_num',16*eel4_num l2=l-2 endif do ll=1,3 -cold ghalf=0.5d0*eel4*ekl*gacont_hbr(ll,jj,i) - ggg1(ll)=eel4*g_contij(ll,1) - ggg2(ll)=eel4*g_contij(ll,2) - ghalf=0.5d0*ggg1(ll) -cd ghalf=0.0d0 - gradcorr(ll,i)=gradcorr(ll,i)+ghalf+ekont*derx(ll,2,1) +cgrad ggg1(ll)=eel4*g_contij(ll,1) +cgrad ggg2(ll)=eel4*g_contij(ll,2) + glongij=eel4*g_contij(ll,1)+ekont*derx(ll,1,1) + glongkl=eel4*g_contij(ll,2)+ekont*derx(ll,1,2) +cgrad ghalf=0.5d0*ggg1(ll) + gradcorr(ll,i)=gradcorr(ll,i)+ekont*derx(ll,2,1) gradcorr(ll,i+1)=gradcorr(ll,i+1)+ekont*derx(ll,3,1) - gradcorr(ll,j)=gradcorr(ll,j)+ghalf+ekont*derx(ll,4,1) + gradcorr(ll,j)=gradcorr(ll,j)+ekont*derx(ll,4,1) gradcorr(ll,j1)=gradcorr(ll,j1)+ekont*derx(ll,5,1) -cold ghalf=0.5d0*eel4*eij*gacont_hbr(ll,kk,k) - ghalf=0.5d0*ggg2(ll) -cd ghalf=0.0d0 - gradcorr(ll,k)=gradcorr(ll,k)+ghalf+ekont*derx(ll,2,2) + gradcorr_long(ll,j)=gradcorr_long(ll,j)+glongij + gradcorr_long(ll,i)=gradcorr_long(ll,i)-glongij +cgrad ghalf=0.5d0*ggg2(ll) + gradcorr(ll,k)=gradcorr(ll,k)+ekont*derx(ll,2,2) gradcorr(ll,k+1)=gradcorr(ll,k+1)+ekont*derx(ll,3,2) - gradcorr(ll,l)=gradcorr(ll,l)+ghalf+ekont*derx(ll,4,2) + gradcorr(ll,l)=gradcorr(ll,l)+ekont*derx(ll,4,2) gradcorr(ll,l1)=gradcorr(ll,l1)+ekont*derx(ll,5,2) + gradcorr_long(ll,l)=gradcorr_long(ll,l)+glongkl + gradcorr_long(ll,k)=gradcorr_long(ll,k)-glongkl enddo -cd goto 1112 - do m=i+1,j-1 - do ll=1,3 -cold gradcorr(ll,m)=gradcorr(ll,m)+eel4*ekl*gacont_hbr(ll,jj,i) - gradcorr(ll,m)=gradcorr(ll,m)+ggg1(ll) - enddo - enddo - do m=k+1,l-1 - do ll=1,3 -cold gradcorr(ll,m)=gradcorr(ll,m)+eel4*eij*gacont_hbr(ll,kk,k) - gradcorr(ll,m)=gradcorr(ll,m)+ggg2(ll) - enddo - enddo -1112 continue - do m=i+2,j2 - do ll=1,3 - gradcorr(ll,m)=gradcorr(ll,m)+ekont*derx(ll,1,1) - enddo - enddo - do m=k+2,l2 - do ll=1,3 - gradcorr(ll,m)=gradcorr(ll,m)+ekont*derx(ll,1,2) - enddo - enddo +cgrad do m=i+1,j-1 +cgrad do ll=1,3 +cgrad gradcorr(ll,m)=gradcorr(ll,m)+ggg1(ll) +cgrad enddo +cgrad enddo +cgrad do m=k+1,l-1 +cgrad do ll=1,3 +cgrad gradcorr(ll,m)=gradcorr(ll,m)+ggg2(ll) +cgrad enddo +cgrad enddo +cgrad do m=i+2,j2 +cgrad do ll=1,3 +cgrad gradcorr(ll,m)=gradcorr(ll,m)+ekont*derx(ll,1,1) +cgrad enddo +cgrad enddo +cgrad do m=k+2,l2 +cgrad do ll=1,3 +cgrad gradcorr(ll,m)=gradcorr(ll,m)+ekont*derx(ll,1,2) +cgrad enddo +cgrad enddo cd do iii=1,nres-3 cd write (2,*) iii,gcorr_loc(iii) cd enddo - endif + endif ! calc_grad eello4=ekont*eel4 cd write (2,*) 'ekont',ekont cd write (iout,*) 'eello4',ekont*eel4 @@ -5718,7 +7293,6 @@ C--------------------------------------------------------------------------- double precision function eello5(i,j,k,l,jj,kk) implicit real*8 (a-h,o-z) include 'DIMENSIONS' - include 'sizesclu.dat' include 'COMMON.IOUNITS' include 'COMMON.CHAIN' include 'COMMON.DERIV' @@ -5767,9 +7341,9 @@ cd endif cd write (iout,*) cd & 'EELLO5: Contacts have occurred for peptide groups',i,j, cd & ' and',k,l - itk=itortyp(itype(k)) - itl=itortyp(itype(l)) - itj=itortyp(itype(j)) + itk=itype2loc(itype(k)) + itl=itype2loc(itype(l)) + itj=itype2loc(itype(j)) eello5_1=0.0d0 eello5_2=0.0d0 eello5_3=0.0d0 @@ -5798,7 +7372,7 @@ cd write (2,*) 'AEAb2',AEAb2(1,1,1),AEAb2(2,1,1) vv(2)=pizda(1,2)+pizda(2,1) eello5_1=scalar2(AEAb2(1,1,1),Ub2(1,k)) & +0.5d0*scalar2(vv(1),Dtobr2(1,i)) - if (calc_grad) then + if (calc_grad) then C Explicit gradient in virtual-dihedral angles. if (i.gt.1) g_corr5_loc(i-1)=g_corr5_loc(i-1) & +ekont*(scalar2(AEAb2derg(1,2,1,1),Ub2(1,k)) @@ -5836,15 +7410,15 @@ C Cartesian gradient enddo enddo enddo + endif ! calc_grad c goto 1112 - endif c1111 continue C Contribution from graph II - call transpose2(EE(1,1,itk),auxmat(1,1)) + call transpose2(EE(1,1,k),auxmat(1,1)) call matmat2(auxmat(1,1),AEA(1,1,1),pizda(1,1)) vv(1)=pizda(1,1)+pizda(2,2) vv(2)=pizda(2,1)-pizda(1,2) - eello5_2=scalar2(AEAb1(1,2,1),b1(1,itk)) + eello5_2=scalar2(AEAb1(1,2,1),b1(1,k)) & -0.5d0*scalar2(vv(1),Ctobr(1,k)) if (calc_grad) then C Explicit gradient in virtual-dihedral angles. @@ -5855,11 +7429,11 @@ C Explicit gradient in virtual-dihedral angles. vv(2)=pizda(2,1)-pizda(1,2) if (l.eq.j+1) then g_corr5_loc(l-1)=g_corr5_loc(l-1) - & +ekont*(scalar2(AEAb1derg(1,2,1),b1(1,itk)) + & +ekont*(scalar2(AEAb1derg(1,2,1),b1(1,k)) & -0.5d0*scalar2(vv(1),Ctobr(1,k))) else g_corr5_loc(j-1)=g_corr5_loc(j-1) - & +ekont*(scalar2(AEAb1derg(1,2,1),b1(1,itk)) + & +ekont*(scalar2(AEAb1derg(1,2,1),b1(1,k)) & -0.5d0*scalar2(vv(1),Ctobr(1,k))) endif C Cartesian gradient @@ -5871,13 +7445,13 @@ C Cartesian gradient vv(1)=pizda(1,1)+pizda(2,2) vv(2)=pizda(2,1)-pizda(1,2) derx(lll,kkk,iii)=derx(lll,kkk,iii) - & +scalar2(AEAb1derx(1,lll,kkk,iii,2,1),b1(1,itk)) + & +scalar2(AEAb1derx(1,lll,kkk,iii,2,1),b1(1,k)) & -0.5d0*scalar2(vv(1),Ctobr(1,k)) enddo enddo enddo + endif ! calc_grad cd goto 1112 - endif cd1111 continue if (l.eq.j+1) then cd goto 1110 @@ -5922,16 +7496,14 @@ C Cartesian gradient enddo enddo cd goto 1112 - endif C Contribution from graph IV cd1110 continue - call transpose2(EE(1,1,itl),auxmat(1,1)) + call transpose2(EE(1,1,l),auxmat(1,1)) call matmat2(auxmat(1,1),AEA(1,1,2),pizda(1,1)) vv(1)=pizda(1,1)+pizda(2,2) vv(2)=pizda(2,1)-pizda(1,2) - eello5_4=scalar2(AEAb1(1,2,2),b1(1,itl)) + eello5_4=scalar2(AEAb1(1,2,2),b1(1,l)) & -0.5d0*scalar2(vv(1),Ctobr(1,l)) - if (calc_grad) then C Explicit gradient in virtual-dihedral angles. g_corr5_loc(l-1)=g_corr5_loc(l-1) & -0.5d0*ekont*scalar2(vv(1),Ctobrder(1,l)) @@ -5939,7 +7511,7 @@ C Explicit gradient in virtual-dihedral angles. vv(1)=pizda(1,1)+pizda(2,2) vv(2)=pizda(2,1)-pizda(1,2) g_corr5_loc(k-1)=g_corr5_loc(k-1) - & +ekont*(scalar2(AEAb1derg(1,2,2),b1(1,itl)) + & +ekont*(scalar2(AEAb1derg(1,2,2),b1(1,l)) & -0.5d0*scalar2(vv(1),Ctobr(1,l))) C Cartesian gradient do iii=1,2 @@ -5950,12 +7522,12 @@ C Cartesian gradient vv(1)=pizda(1,1)+pizda(2,2) vv(2)=pizda(2,1)-pizda(1,2) derx(lll,kkk,iii)=derx(lll,kkk,iii) - & +scalar2(AEAb1derx(1,lll,kkk,iii,2,2),b1(1,itl)) + & +scalar2(AEAb1derx(1,lll,kkk,iii,2,2),b1(1,l)) & -0.5d0*scalar2(vv(1),Ctobr(1,l)) enddo enddo enddo - endif + endif ! calc_grad else C Antiparallel orientation C Contribution from graph III @@ -5998,15 +7570,15 @@ C Cartesian gradient enddo enddo enddo + endif ! calc_grad cd goto 1112 - endif C Contribution from graph IV 1110 continue - call transpose2(EE(1,1,itj),auxmat(1,1)) + call transpose2(EE(1,1,j),auxmat(1,1)) call matmat2(auxmat(1,1),AEA(1,1,2),pizda(1,1)) vv(1)=pizda(1,1)+pizda(2,2) vv(2)=pizda(2,1)-pizda(1,2) - eello5_4=scalar2(AEAb1(1,2,2),b1(1,itj)) + eello5_4=scalar2(AEAb1(1,2,2),b1(1,j)) & -0.5d0*scalar2(vv(1),Ctobr(1,j)) if (calc_grad) then C Explicit gradient in virtual-dihedral angles. @@ -6016,7 +7588,7 @@ C Explicit gradient in virtual-dihedral angles. vv(1)=pizda(1,1)+pizda(2,2) vv(2)=pizda(2,1)-pizda(1,2) g_corr5_loc(k-1)=g_corr5_loc(k-1) - & +ekont*(scalar2(AEAb1derg(1,2,2),b1(1,itj)) + & +ekont*(scalar2(AEAb1derg(1,2,2),b1(1,j)) & -0.5d0*scalar2(vv(1),Ctobr(1,j))) C Cartesian gradient do iii=1,2 @@ -6027,12 +7599,12 @@ C Cartesian gradient vv(1)=pizda(1,1)+pizda(2,2) vv(2)=pizda(2,1)-pizda(1,2) derx(lll,kkk,3-iii)=derx(lll,kkk,3-iii) - & +scalar2(AEAb1derx(1,lll,kkk,iii,2,2),b1(1,itj)) + & +scalar2(AEAb1derx(1,lll,kkk,iii,2,2),b1(1,j)) & -0.5d0*scalar2(vv(1),Ctobr(1,j)) enddo enddo enddo - endif + endif ! calc_grad endif 1112 continue eel5=eello5_1+eello5_2+eello5_3+eello5_4 @@ -6064,52 +7636,70 @@ cd eij=1.0d0 cd ekl=1.0d0 cd ekont=1.0d0 cd write (2,*) 'eij',eij,' ekl',ekl,' ekont',ekont +C 2/11/08 AL Gradients over DC's connecting interacting sites will be +C summed up outside the subrouine as for the other subroutines +C handling long-range interactions. The old code is commented out +C with "cgrad" to keep track of changes. do ll=1,3 - ggg1(ll)=eel5*g_contij(ll,1) - ggg2(ll)=eel5*g_contij(ll,2) +cgrad ggg1(ll)=eel5*g_contij(ll,1) +cgrad ggg2(ll)=eel5*g_contij(ll,2) + gradcorr5ij=eel5*g_contij(ll,1)+ekont*derx(ll,1,1) + gradcorr5kl=eel5*g_contij(ll,2)+ekont*derx(ll,1,2) +c write (iout,'(a,3i3,a,5f8.3,2i3,a,5f8.3,a,f8.3)') +c & "ecorr5",ll,i,j," derx",derx(ll,2,1),derx(ll,3,1),derx(ll,4,1), +c & derx(ll,5,1),k,l," derx",derx(ll,2,2),derx(ll,3,2), +c & derx(ll,4,2),derx(ll,5,2)," ekont",ekont +c write (iout,'(a,3i3,a,3f8.3,2i3,a,3f8.3)') +c & "ecorr5",ll,i,j," gradcorr5",g_contij(ll,1),derx(ll,1,1), +c & gradcorr5ij, +c & k,l," gradcorr5",g_contij(ll,2),derx(ll,1,2),gradcorr5kl cold ghalf=0.5d0*eel5*ekl*gacont_hbr(ll,jj,i) - ghalf=0.5d0*ggg1(ll) +cgrad ghalf=0.5d0*ggg1(ll) cd ghalf=0.0d0 - gradcorr5(ll,i)=gradcorr5(ll,i)+ghalf+ekont*derx(ll,2,1) + gradcorr5(ll,i)=gradcorr5(ll,i)+ekont*derx(ll,2,1) gradcorr5(ll,i+1)=gradcorr5(ll,i+1)+ekont*derx(ll,3,1) - gradcorr5(ll,j)=gradcorr5(ll,j)+ghalf+ekont*derx(ll,4,1) + gradcorr5(ll,j)=gradcorr5(ll,j)+ekont*derx(ll,4,1) gradcorr5(ll,j1)=gradcorr5(ll,j1)+ekont*derx(ll,5,1) + gradcorr5_long(ll,j)=gradcorr5_long(ll,j)+gradcorr5ij + gradcorr5_long(ll,i)=gradcorr5_long(ll,i)-gradcorr5ij cold ghalf=0.5d0*eel5*eij*gacont_hbr(ll,kk,k) - ghalf=0.5d0*ggg2(ll) +cgrad ghalf=0.5d0*ggg2(ll) cd ghalf=0.0d0 - gradcorr5(ll,k)=gradcorr5(ll,k)+ghalf+ekont*derx(ll,2,2) + gradcorr5(ll,k)=gradcorr5(ll,k)+ekont*derx(ll,2,2) gradcorr5(ll,k+1)=gradcorr5(ll,k+1)+ekont*derx(ll,3,2) - gradcorr5(ll,l)=gradcorr5(ll,l)+ghalf+ekont*derx(ll,4,2) + gradcorr5(ll,l)=gradcorr5(ll,l)+ekont*derx(ll,4,2) gradcorr5(ll,l1)=gradcorr5(ll,l1)+ekont*derx(ll,5,2) + gradcorr5_long(ll,l)=gradcorr5_long(ll,l)+gradcorr5kl + gradcorr5_long(ll,k)=gradcorr5_long(ll,k)-gradcorr5kl enddo + endif ! calc_grad cd goto 1112 - do m=i+1,j-1 - do ll=1,3 +cgrad do m=i+1,j-1 +cgrad do ll=1,3 cold gradcorr5(ll,m)=gradcorr5(ll,m)+eel5*ekl*gacont_hbr(ll,jj,i) - gradcorr5(ll,m)=gradcorr5(ll,m)+ggg1(ll) - enddo - enddo - do m=k+1,l-1 - do ll=1,3 +cgrad gradcorr5(ll,m)=gradcorr5(ll,m)+ggg1(ll) +cgrad enddo +cgrad enddo +cgrad do m=k+1,l-1 +cgrad do ll=1,3 cold gradcorr5(ll,m)=gradcorr5(ll,m)+eel5*eij*gacont_hbr(ll,kk,k) - gradcorr5(ll,m)=gradcorr5(ll,m)+ggg2(ll) - enddo - enddo +cgrad gradcorr5(ll,m)=gradcorr5(ll,m)+ggg2(ll) +cgrad enddo +cgrad enddo c1112 continue - do m=i+2,j2 - do ll=1,3 - gradcorr5(ll,m)=gradcorr5(ll,m)+ekont*derx(ll,1,1) - enddo - enddo - do m=k+2,l2 - do ll=1,3 - gradcorr5(ll,m)=gradcorr5(ll,m)+ekont*derx(ll,1,2) - enddo - enddo +cgrad do m=i+2,j2 +cgrad do ll=1,3 +cgrad gradcorr5(ll,m)=gradcorr5(ll,m)+ekont*derx(ll,1,1) +cgrad enddo +cgrad enddo +cgrad do m=k+2,l2 +cgrad do ll=1,3 +cgrad gradcorr5(ll,m)=gradcorr5(ll,m)+ekont*derx(ll,1,2) +cgrad enddo +cgrad enddo cd do iii=1,nres-3 cd write (2,*) iii,g_corr5_loc(iii) cd enddo - endif eello5=ekont*eel5 cd write (2,*) 'ekont',ekont cd write (iout,*) 'eello5',ekont*eel5 @@ -6119,7 +7709,6 @@ c-------------------------------------------------------------------------- double precision function eello6(i,j,k,l,jj,kk) implicit real*8 (a-h,o-z) include 'DIMENSIONS' - include 'sizesclu.dat' include 'COMMON.IOUNITS' include 'COMMON.CHAIN' include 'COMMON.DERIV' @@ -6179,12 +7768,12 @@ cd ekont=1.0d0 endif C If turn contributions are considered, they will be handled separately. eel6=eello6_1+eello6_2+eello6_3+eello6_4+eello6_5+eello6_6 -cd write(iout,*) 'eello6_1',eello6_1,' eel6_1_num',16*eel6_1_num -cd write(iout,*) 'eello6_2',eello6_2,' eel6_2_num',16*eel6_2_num -cd write(iout,*) 'eello6_3',eello6_3,' eel6_3_num',16*eel6_3_num -cd write(iout,*) 'eello6_4',eello6_4,' eel6_4_num',16*eel6_4_num -cd write(iout,*) 'eello6_5',eello6_5,' eel6_5_num',16*eel6_5_num -cd write(iout,*) 'eello6_6',eello6_6,' eel6_6_num',16*eel6_6_num +cd write(iout,*) 'eello6_1',eello6_1!,' eel6_1_num',16*eel6_1_num +cd write(iout,*) 'eello6_2',eello6_2!,' eel6_2_num',16*eel6_2_num +cd write(iout,*) 'eello6_3',eello6_3!,' eel6_3_num',16*eel6_3_num +cd write(iout,*) 'eello6_4',eello6_4!,' eel6_4_num',16*eel6_4_num +cd write(iout,*) 'eello6_5',eello6_5!,' eel6_5_num',16*eel6_5_num +cd write(iout,*) 'eello6_6',eello6_6!,' eel6_6_num',16*eel6_6_num cd goto 1112 if (calc_grad) then if (j.lt.nres-1) then @@ -6202,51 +7791,57 @@ cd goto 1112 l2=l-2 endif do ll=1,3 - ggg1(ll)=eel6*g_contij(ll,1) - ggg2(ll)=eel6*g_contij(ll,2) +cgrad ggg1(ll)=eel6*g_contij(ll,1) +cgrad ggg2(ll)=eel6*g_contij(ll,2) cold ghalf=0.5d0*eel6*ekl*gacont_hbr(ll,jj,i) - ghalf=0.5d0*ggg1(ll) +cgrad ghalf=0.5d0*ggg1(ll) cd ghalf=0.0d0 - gradcorr6(ll,i)=gradcorr6(ll,i)+ghalf+ekont*derx(ll,2,1) + gradcorr6ij=eel6*g_contij(ll,1)+ekont*derx(ll,1,1) + gradcorr6kl=eel6*g_contij(ll,2)+ekont*derx(ll,1,2) + gradcorr6(ll,i)=gradcorr6(ll,i)+ekont*derx(ll,2,1) gradcorr6(ll,i+1)=gradcorr6(ll,i+1)+ekont*derx(ll,3,1) - gradcorr6(ll,j)=gradcorr6(ll,j)+ghalf+ekont*derx(ll,4,1) + gradcorr6(ll,j)=gradcorr6(ll,j)+ekont*derx(ll,4,1) gradcorr6(ll,j1)=gradcorr6(ll,j1)+ekont*derx(ll,5,1) - ghalf=0.5d0*ggg2(ll) + gradcorr6_long(ll,j)=gradcorr6_long(ll,j)+gradcorr6ij + gradcorr6_long(ll,i)=gradcorr6_long(ll,i)-gradcorr6ij +cgrad ghalf=0.5d0*ggg2(ll) cold ghalf=0.5d0*eel6*eij*gacont_hbr(ll,kk,k) cd ghalf=0.0d0 - gradcorr6(ll,k)=gradcorr6(ll,k)+ghalf+ekont*derx(ll,2,2) + gradcorr6(ll,k)=gradcorr6(ll,k)+ekont*derx(ll,2,2) gradcorr6(ll,k+1)=gradcorr6(ll,k+1)+ekont*derx(ll,3,2) - gradcorr6(ll,l)=gradcorr6(ll,l)+ghalf+ekont*derx(ll,4,2) + gradcorr6(ll,l)=gradcorr6(ll,l)+ekont*derx(ll,4,2) gradcorr6(ll,l1)=gradcorr6(ll,l1)+ekont*derx(ll,5,2) + gradcorr6_long(ll,l)=gradcorr6_long(ll,l)+gradcorr6kl + gradcorr6_long(ll,k)=gradcorr6_long(ll,k)-gradcorr6kl enddo + endif ! calc_grad cd goto 1112 - do m=i+1,j-1 - do ll=1,3 +cgrad do m=i+1,j-1 +cgrad do ll=1,3 cold gradcorr6(ll,m)=gradcorr6(ll,m)+eel6*ekl*gacont_hbr(ll,jj,i) - gradcorr6(ll,m)=gradcorr6(ll,m)+ggg1(ll) - enddo - enddo - do m=k+1,l-1 - do ll=1,3 +cgrad gradcorr6(ll,m)=gradcorr6(ll,m)+ggg1(ll) +cgrad enddo +cgrad enddo +cgrad do m=k+1,l-1 +cgrad do ll=1,3 cold gradcorr6(ll,m)=gradcorr6(ll,m)+eel6*eij*gacont_hbr(ll,kk,k) - gradcorr6(ll,m)=gradcorr6(ll,m)+ggg2(ll) - enddo - enddo -1112 continue - do m=i+2,j2 - do ll=1,3 - gradcorr6(ll,m)=gradcorr6(ll,m)+ekont*derx(ll,1,1) - enddo - enddo - do m=k+2,l2 - do ll=1,3 - gradcorr6(ll,m)=gradcorr6(ll,m)+ekont*derx(ll,1,2) - enddo - enddo +cgrad gradcorr6(ll,m)=gradcorr6(ll,m)+ggg2(ll) +cgrad enddo +cgrad enddo +cgrad1112 continue +cgrad do m=i+2,j2 +cgrad do ll=1,3 +cgrad gradcorr6(ll,m)=gradcorr6(ll,m)+ekont*derx(ll,1,1) +cgrad enddo +cgrad enddo +cgrad do m=k+2,l2 +cgrad do ll=1,3 +cgrad gradcorr6(ll,m)=gradcorr6(ll,m)+ekont*derx(ll,1,2) +cgrad enddo +cgrad enddo cd do iii=1,nres-3 cd write (2,*) iii,g_corr6_loc(iii) cd enddo - endif eello6=ekont*eel6 cd write (2,*) 'ekont',ekont cd write (iout,*) 'eello6',ekont*eel6 @@ -6256,7 +7851,6 @@ c-------------------------------------------------------------------------- double precision function eello6_graph1(i,j,k,l,imat,swap) implicit real*8 (a-h,o-z) include 'DIMENSIONS' - include 'sizesclu.dat' include 'COMMON.IOUNITS' include 'COMMON.CHAIN' include 'COMMON.DERIV' @@ -6270,20 +7864,20 @@ c-------------------------------------------------------------------------- logical lprn common /kutas/ lprn CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC -C -C Parallel Antiparallel -C -C o o -C /l\ /j\ -C / \ / \ -C /| o | | o |\ -C \ j|/k\| / \ |/k\|l / -C \ / \ / \ / \ / -C o o 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 |\ C +C \ j|/k\| / \ |/k\|l / C +C \ / \ / \ / \ / C +C o o o o C +C i i C +C C CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC - itk=itortyp(itype(k)) + itk=itype2loc(itype(k)) s1= scalar2(AEAb1(1,2,imat),CUgb2(1,i)) s2=-scalar2(AEAb2(1,1,imat),Ug2Db1t(1,k)) s3= scalar2(AEAb2(1,1,imat),CUgb2(1,k)) @@ -6292,12 +7886,12 @@ CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC vv1(1)=pizda1(1,1)-pizda1(2,2) vv1(2)=pizda1(1,2)+pizda1(2,1) s4=0.5d0*scalar2(vv1(1),Dtobr2(1,i)) - vv(1)=AEAb1(1,2,imat)*b1(1,itk)-AEAb1(2,2,imat)*b1(2,itk) - vv(2)=AEAb1(1,2,imat)*b1(2,itk)+AEAb1(2,2,imat)*b1(1,itk) + vv(1)=AEAb1(1,2,imat)*b1(1,k)-AEAb1(2,2,imat)*b1(2,k) + vv(2)=AEAb1(1,2,imat)*b1(2,k)+AEAb1(2,2,imat)*b1(1,k) s5=scalar2(vv(1),Dtobr2(1,i)) cd write (2,*) 's1',s1,' s2',s2,' s3',s3,' s4', s4,' s5',s5 eello6_graph1=-0.5d0*(s1+s2+s3+s4+s5) - if (.not. calc_grad) return + if (calc_grad) then if (i.gt.1) g_corr6_loc(i-1)=g_corr6_loc(i-1) & -0.5d0*ekont*(scalar2(AEAb1(1,2,imat),CUgb2der(1,i)) & -scalar2(AEAb2derg(1,2,1,imat),Ug2Db1t(1,k)) @@ -6307,8 +7901,8 @@ cd write (2,*) 's1',s1,' s2',s2,' s3',s3,' s4', s4,' s5',s5 call matmat2(AEAderg(1,1,imat),auxmat(1,1),pizda1(1,1)) vv1(1)=pizda1(1,1)-pizda1(2,2) vv1(2)=pizda1(1,2)+pizda1(2,1) - vv(1)=AEAb1derg(1,2,imat)*b1(1,itk)-AEAb1derg(2,2,imat)*b1(2,itk) - vv(2)=AEAb1derg(1,2,imat)*b1(2,itk)+AEAb1derg(2,2,imat)*b1(1,itk) + vv(1)=AEAb1derg(1,2,imat)*b1(1,k)-AEAb1derg(2,2,imat)*b1(2,k) + vv(2)=AEAb1derg(1,2,imat)*b1(2,k)+AEAb1derg(2,2,imat)*b1(1,k) if (l.eq.j+1) then g_corr6_loc(l-1)=g_corr6_loc(l-1) & +ekont*(-0.5d0*(scalar2(AEAb1derg(1,2,imat),CUgb2(1,i)) @@ -6347,22 +7941,22 @@ cd write (2,*) 's1',s1,' s2',s2,' s3',s3,' s4', s4,' s5',s5 vv1(1)=pizda1(1,1)-pizda1(2,2) vv1(2)=pizda1(1,2)+pizda1(2,1) s4=0.5d0*scalar2(vv1(1),Dtobr2(1,i)) - vv(1)=AEAb1derx(1,lll,kkk,iii,2,imat)*b1(1,itk) - & -AEAb1derx(2,lll,kkk,iii,2,imat)*b1(2,itk) - vv(2)=AEAb1derx(1,lll,kkk,iii,2,imat)*b1(2,itk) - & +AEAb1derx(2,lll,kkk,iii,2,imat)*b1(1,itk) + vv(1)=AEAb1derx(1,lll,kkk,iii,2,imat)*b1(1,k) + & -AEAb1derx(2,lll,kkk,iii,2,imat)*b1(2,k) + vv(2)=AEAb1derx(1,lll,kkk,iii,2,imat)*b1(2,k) + & +AEAb1derx(2,lll,kkk,iii,2,imat)*b1(1,k) s5=scalar2(vv(1),Dtobr2(1,i)) derx(lll,kkk,ind)=derx(lll,kkk,ind)-0.5d0*(s1+s2+s3+s4+s5) enddo enddo enddo + endif ! calc_grad return end c---------------------------------------------------------------------------- double precision function eello6_graph2(i,j,k,l,jj,kk,swap) implicit real*8 (a-h,o-z) include 'DIMENSIONS' - include 'sizesclu.dat' include 'COMMON.IOUNITS' include 'COMMON.CHAIN' include 'COMMON.DERIV' @@ -6373,22 +7967,22 @@ 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, @@ -6412,8 +8006,8 @@ cd write (2,*) 'eello6_graph2:','s1',s1,' s2',s2,' s3',s3,' s4',s4 eello6_graph2=-(s2+s3+s4) #endif c eello6_graph2=-s3 - if (.not. calc_grad) return C Derivatives in gamma(i-1) + if (calc_grad) then if (i.gt.1) then #ifdef MOMENT s1=dipderg(1,jj,i)*dip(1,kk,k) @@ -6543,13 +8137,13 @@ cd write (2,*) 's1',s1,' s2',s2,' s3',s3,' s4',s4 enddo enddo enddo + endif ! calc_grad return end c---------------------------------------------------------------------------- double precision function eello6_graph3(i,j,k,l,jj,kk,swap) implicit real*8 (a-h,o-z) include 'DIMENSIONS' - include 'sizesclu.dat' include 'COMMON.IOUNITS' include 'COMMON.CHAIN' include 'COMMON.DERIV' @@ -6561,63 +8155,64 @@ 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 C energy moment and not to the cluster cumulant. iti=itortyp(itype(i)) if (j.lt.nres-1) then - itj1=itortyp(itype(j+1)) + itj1=itype2loc(itype(j+1)) else - itj1=ntortyp+1 + itj1=nloctyp endif - itk=itortyp(itype(k)) - itk1=itortyp(itype(k+1)) + itk=itype2loc(itype(k)) + itk1=itype2loc(itype(k+1)) if (l.lt.nres-1) then - itl1=itortyp(itype(l+1)) + itl1=itype2loc(itype(l+1)) else - itl1=ntortyp+1 + itl1=nloctyp endif #ifdef MOMENT s1=dip(4,jj,i)*dip(4,kk,k) #endif - call matvec2(AECA(1,1,1),b1(1,itk1),auxvec(1)) - s2=0.5d0*scalar2(b1(1,itk),auxvec(1)) - call matvec2(AECA(1,1,2),b1(1,itl1),auxvec(1)) - s3=0.5d0*scalar2(b1(1,itj1),auxvec(1)) - call transpose2(EE(1,1,itk),auxmat(1,1)) + call matvec2(AECA(1,1,1),b1(1,k+1),auxvec(1)) + s2=0.5d0*scalar2(b1(1,k),auxvec(1)) + call matvec2(AECA(1,1,2),b1(1,l+1),auxvec(1)) + s3=0.5d0*scalar2(b1(1,j+1),auxvec(1)) + call transpose2(EE(1,1,k),auxmat(1,1)) call matmat2(auxmat(1,1),AECA(1,1,1),pizda(1,1)) vv(1)=pizda(1,1)+pizda(2,2) vv(2)=pizda(2,1)-pizda(1,2) s4=-0.25d0*scalar2(vv(1),Ctobr(1,k)) -cd write (2,*) 'eello6_graph3:','s1',s1,' s2',s2,' s3',s3,' s4',s4 +cd write (2,*) 'eello6_graph3:','s1',s1,' s2',s2,' s3',s3,' s4',s4, +cd & "sum",-(s2+s3+s4) #ifdef MOMENT eello6_graph3=-(s1+s2+s3+s4) #else eello6_graph3=-(s2+s3+s4) #endif c eello6_graph3=-s4 - if (.not. calc_grad) return C Derivatives in gamma(k-1) - call matvec2(AECAderg(1,1,2),b1(1,itl1),auxvec(1)) - s3=0.5d0*scalar2(b1(1,itj1),auxvec(1)) + if (calc_grad) then + call matvec2(AECAderg(1,1,2),b1(1,l+1),auxvec(1)) + s3=0.5d0*scalar2(b1(1,j+1),auxvec(1)) s4=-0.25d0*scalar2(vv(1),Ctobrder(1,k)) g_corr6_loc(k-1)=g_corr6_loc(k-1)-ekont*(s3+s4) C Derivatives in gamma(l-1) - call matvec2(AECAderg(1,1,1),b1(1,itk1),auxvec(1)) - s2=0.5d0*scalar2(b1(1,itk),auxvec(1)) + call matvec2(AECAderg(1,1,1),b1(1,k+1),auxvec(1)) + s2=0.5d0*scalar2(b1(1,k),auxvec(1)) call matmat2(auxmat(1,1),AECAderg(1,1,1),pizda(1,1)) vv(1)=pizda(1,1)+pizda(2,2) vv(2)=pizda(2,1)-pizda(1,2) @@ -6634,12 +8229,12 @@ C Cartesian derivatives. s1=dip(4,jj,i)*dipderx(lll,kkk,4,kk,k) endif #endif - call matvec2(AECAderx(1,1,lll,kkk,iii,1),b1(1,itk1), + call matvec2(AECAderx(1,1,lll,kkk,iii,1),b1(1,k+1), & auxvec(1)) - s2=0.5d0*scalar2(b1(1,itk),auxvec(1)) - call matvec2(AECAderx(1,1,lll,kkk,iii,2),b1(1,itl1), + s2=0.5d0*scalar2(b1(1,k),auxvec(1)) + call matvec2(AECAderx(1,1,lll,kkk,iii,2),b1(1,l+1), & auxvec(1)) - s3=0.5d0*scalar2(b1(1,itj1),auxvec(1)) + s3=0.5d0*scalar2(b1(1,j+1),auxvec(1)) call matmat2(auxmat(1,1),AECAderx(1,1,lll,kkk,iii,1), & pizda(1,1)) vv(1)=pizda(1,1)+pizda(2,2) @@ -6659,13 +8254,13 @@ c derx(lll,kkk,iii)=derx(lll,kkk,iii)-s4 enddo enddo enddo + endif ! calc_grad return end c---------------------------------------------------------------------------- double precision function eello6_graph4(i,j,k,l,jj,kk,imat,swap) implicit real*8 (a-h,o-z) include 'DIMENSIONS' - include 'sizesclu.dat' include 'COMMON.IOUNITS' include 'COMMON.CHAIN' include 'COMMON.DERIV' @@ -6679,41 +8274,41 @@ 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 C energy moment and not to the cluster cumulant. cd write (2,*) 'eello_graph4: wturn6',wturn6 - iti=itortyp(itype(i)) - itj=itortyp(itype(j)) + iti=itype2loc(itype(i)) + itj=itype2loc(itype(j)) if (j.lt.nres-1) then - itj1=itortyp(itype(j+1)) + itj1=itype2loc(itype(j+1)) else - itj1=ntortyp+1 + itj1=nloctyp endif - itk=itortyp(itype(k)) + itk=itype2loc(itype(k)) if (k.lt.nres-1) then - itk1=itortyp(itype(k+1)) + itk1=itype2loc(itype(k+1)) else - itk1=ntortyp+1 + itk1=nloctyp endif - itl=itortyp(itype(l)) + itl=itype2loc(itype(l)) if (l.lt.nres-1) then - itl1=itortyp(itype(l+1)) + itl1=itype2loc(itype(l+1)) else - itl1=ntortyp+1 + itl1=nloctyp 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, @@ -6728,11 +8323,11 @@ cd & ' itl',itl,' itl1',itl1 call matvec2(AECA(1,1,imat),Ub2(1,k),auxvec(1)) s2=0.5d0*scalar2(Ub2(1,i),auxvec(1)) if (j.eq.l+1) then - call matvec2(ADtEA1(1,1,3-imat),b1(1,itj1),auxvec1(1)) - s3=-0.5d0*scalar2(b1(1,itj),auxvec1(1)) + call matvec2(ADtEA1(1,1,3-imat),b1(1,j+1),auxvec1(1)) + s3=-0.5d0*scalar2(b1(1,j),auxvec1(1)) else - call matvec2(ADtEA1(1,1,3-imat),b1(1,itl1),auxvec1(1)) - s3=-0.5d0*scalar2(b1(1,itl),auxvec1(1)) + call matvec2(ADtEA1(1,1,3-imat),b1(1,l+1),auxvec1(1)) + s3=-0.5d0*scalar2(b1(1,l),auxvec1(1)) endif call transpose2(EUg(1,1,k),auxmat(1,1)) call matmat2(AECA(1,1,imat),auxmat(1,1),pizda(1,1)) @@ -6745,8 +8340,8 @@ cd write (2,*) 'eello6_graph4:','s1',s1,' s2',s2,' s3',s3,' s4',s4 #else eello6_graph4=-(s2+s3+s4) #endif - if (.not. calc_grad) return C Derivatives in gamma(i-1) + if (calc_grad) then if (i.gt.1) then #ifdef MOMENT if (imat.eq.1) then @@ -6757,11 +8352,11 @@ C Derivatives in gamma(i-1) #endif s2=0.5d0*scalar2(Ub2der(1,i),auxvec(1)) if (j.eq.l+1) then - call matvec2(ADtEA1derg(1,1,1,3-imat),b1(1,itj1),auxvec1(1)) - s3=-0.5d0*scalar2(b1(1,itj),auxvec1(1)) + call matvec2(ADtEA1derg(1,1,1,3-imat),b1(1,j+1),auxvec1(1)) + s3=-0.5d0*scalar2(b1(1,j),auxvec1(1)) else - call matvec2(ADtEA1derg(1,1,1,3-imat),b1(1,itl1),auxvec1(1)) - s3=-0.5d0*scalar2(b1(1,itl),auxvec1(1)) + call matvec2(ADtEA1derg(1,1,1,3-imat),b1(1,l+1),auxvec1(1)) + s3=-0.5d0*scalar2(b1(1,l),auxvec1(1)) endif s4=0.25d0*scalar2(vv(1),Dtobr2der(1,i)) if (wturn6.gt.0.0d0 .and. k.eq.l+4 .and. i.eq.j+2) then @@ -6790,11 +8385,11 @@ C Derivatives in gamma(k-1) call matvec2(AECA(1,1,imat),Ub2der(1,k),auxvec1(1)) s2=0.5d0*scalar2(Ub2(1,i),auxvec1(1)) if (j.eq.l+1) then - call matvec2(ADtEA1derg(1,1,2,3-imat),b1(1,itj1),auxvec1(1)) - s3=-0.5d0*scalar2(b1(1,itj),auxvec1(1)) + call matvec2(ADtEA1derg(1,1,2,3-imat),b1(1,j+1),auxvec1(1)) + s3=-0.5d0*scalar2(b1(1,j),auxvec1(1)) else - call matvec2(ADtEA1derg(1,1,2,3-imat),b1(1,itl1),auxvec1(1)) - s3=-0.5d0*scalar2(b1(1,itl),auxvec1(1)) + call matvec2(ADtEA1derg(1,1,2,3-imat),b1(1,l+1),auxvec1(1)) + s3=-0.5d0*scalar2(b1(1,l),auxvec1(1)) endif call transpose2(EUgder(1,1,k),auxmat1(1,1)) call matmat2(AECA(1,1,imat),auxmat1(1,1),pizda(1,1)) @@ -6860,12 +8455,12 @@ C Cartesian derivatives. s2=0.5d0*scalar2(Ub2(1,i),auxvec(1)) if (j.eq.l+1) then call matvec2(ADtEA1derx(1,1,lll,kkk,iii,3-imat), - & b1(1,itj1),auxvec(1)) - s3=-0.5d0*scalar2(b1(1,itj),auxvec(1)) + & b1(1,j+1),auxvec(1)) + s3=-0.5d0*scalar2(b1(1,j),auxvec(1)) else call matvec2(ADtEA1derx(1,1,lll,kkk,iii,3-imat), - & b1(1,itl1),auxvec(1)) - s3=-0.5d0*scalar2(b1(1,itl),auxvec(1)) + & b1(1,l+1),auxvec(1)) + s3=-0.5d0*scalar2(b1(1,l),auxvec(1)) endif call matmat2(AECAderx(1,1,lll,kkk,iii,imat),auxmat(1,1), & pizda(1,1)) @@ -6905,13 +8500,13 @@ C Cartesian derivatives. enddo enddo enddo + endif ! calc_grad return end c---------------------------------------------------------------------------- double precision function eello_turn6(i,jj,kk) implicit real*8 (a-h,o-z) include 'DIMENSIONS' - include 'sizesclu.dat' include 'COMMON.IOUNITS' include 'COMMON.CHAIN' include 'COMMON.DERIV' @@ -6927,15 +8522,19 @@ c---------------------------------------------------------------------------- & atempd(2,2),auxmatd(2,2),achuj_tempd(2,2),gtempd(2,2),gvecd(2) C 4/7/01 AL Components s1, s8, and s13 were removed, because they pertain to C the respective energy moment and not to the cluster cumulant. + s1=0.0d0 + s8=0.0d0 + s13=0.0d0 +c eello_turn6=0.0d0 j=i+4 k=i+1 l=i+3 - iti=itortyp(itype(i)) - itk=itortyp(itype(k)) - itk1=itortyp(itype(k+1)) - itl=itortyp(itype(l)) - itj=itortyp(itype(j)) + iti=itype2loc(itype(i)) + itk=itype2loc(itype(k)) + itk1=itype2loc(itype(k+1)) + itl=itype2loc(itype(l)) + itj=itype2loc(itype(j)) cd write (2,*) 'itk',itk,' itk1',itk1,' itl',itl,' itj',itj cd write (2,*) 'i',i,' k',k,' j',j,' l',l cd if (i.ne.1 .or. j.ne.3 .or. k.ne.2 .or. l.ne.4) then @@ -6962,21 +8561,17 @@ cd write (2,*) 'eello6_5',eello6_5 #ifdef MOMENT call transpose2(AEA(1,1,1),auxmat(1,1)) call matmat2(EUg(1,1,i+1),auxmat(1,1),auxmat(1,1)) - ss1=scalar2(Ub2(1,i+2),b1(1,itl)) + ss1=scalar2(Ub2(1,i+2),b1(1,l)) s1 = (auxmat(1,1)+auxmat(2,2))*ss1 -#else - s1 = 0.0d0 #endif - call matvec2(EUg(1,1,i+2),b1(1,itl),vtemp1(1)) + call matvec2(EUg(1,1,i+2),b1(1,l),vtemp1(1)) call matvec2(AEA(1,1,1),vtemp1(1),vtemp1(1)) - s2 = scalar2(b1(1,itk),vtemp1(1)) + s2 = scalar2(b1(1,k),vtemp1(1)) #ifdef MOMENT call transpose2(AEA(1,1,2),atemp(1,1)) call matmat2(atemp(1,1),EUg(1,1,i+4),atemp(1,1)) - call matvec2(Ug2(1,1,i+2),dd(1,1,itk1),vtemp2(1)) - s8 = -(atemp(1,1)+atemp(2,2))*scalar2(cc(1,1,itl),vtemp2(1)) -#else - s8=0.0d0 + call matvec2(Ug2(1,1,i+2),dd(1,1,k+1),vtemp2(1)) + s8 = -(atemp(1,1)+atemp(2,2))*scalar2(cc(1,1,l),vtemp2(1)) #endif call matmat2(EUg(1,1,i+3),AEA(1,1,2),auxmat(1,1)) call matvec2(auxmat(1,1),Ub2(1,i+4),vtemp3(1)) @@ -6986,10 +8581,8 @@ cd write (2,*) 'eello6_5',eello6_5 call matmat2(achuj_temp(1,1),EUg(1,1,i+2),gtemp(1,1)) call matmat2(gtemp(1,1),EUg(1,1,i+3),gtemp(1,1)) call matvec2(a_chuj(1,1,jj,i),Ub2(1,i+4),vtemp4(1)) - ss13 = scalar2(b1(1,itk),vtemp4(1)) + ss13 = scalar2(b1(1,k),vtemp4(1)) s13 = (gtemp(1,1)+gtemp(2,2))*ss13 -#else - s13=0.0d0 #endif c write (2,*) 's1,s2,s8,s12,s13',s1,s2,s8,s12,s13 c s1=0.0d0 @@ -6998,17 +8591,17 @@ c s8=0.0d0 c s12=0.0d0 c s13=0.0d0 eel_turn6 = eello6_5 - 0.5d0*(s1+s2+s12+s8+s13) - if (calc_grad) then C Derivatives in gamma(i+2) + if (calc_grad) then + s1d =0.0d0 + s8d =0.0d0 #ifdef MOMENT call transpose2(AEA(1,1,1),auxmatd(1,1)) call matmat2(EUgder(1,1,i+1),auxmatd(1,1),auxmatd(1,1)) s1d = (auxmatd(1,1)+auxmatd(2,2))*ss1 call transpose2(AEAderg(1,1,2),atempd(1,1)) call matmat2(atempd(1,1),EUg(1,1,i+4),atempd(1,1)) - s8d = -(atempd(1,1)+atempd(2,2))*scalar2(cc(1,1,itl),vtemp2(1)) -#else - s8d=0.0d0 + s8d = -(atempd(1,1)+atempd(2,2))*scalar2(cc(1,1,l),vtemp2(1)) #endif call matmat2(EUg(1,1,i+3),AEAderg(1,1,2),auxmatd(1,1)) call matvec2(auxmatd(1,1),Ub2(1,i+4),vtemp3d(1)) @@ -7023,25 +8616,21 @@ C Derivatives in gamma(i+3) #ifdef MOMENT call transpose2(AEA(1,1,1),auxmatd(1,1)) call matmat2(EUg(1,1,i+1),auxmatd(1,1),auxmatd(1,1)) - ss1d=scalar2(Ub2der(1,i+2),b1(1,itl)) + ss1d=scalar2(Ub2der(1,i+2),b1(1,l)) s1d = (auxmatd(1,1)+auxmatd(2,2))*ss1d -#else - s1d=0.0d0 #endif - call matvec2(EUgder(1,1,i+2),b1(1,itl),vtemp1d(1)) + call matvec2(EUgder(1,1,i+2),b1(1,l),vtemp1d(1)) call matvec2(AEA(1,1,1),vtemp1d(1),vtemp1d(1)) - s2d = scalar2(b1(1,itk),vtemp1d(1)) + s2d = scalar2(b1(1,k),vtemp1d(1)) #ifdef MOMENT - call matvec2(Ug2der(1,1,i+2),dd(1,1,itk1),vtemp2d(1)) - s8d = -(atemp(1,1)+atemp(2,2))*scalar2(cc(1,1,itl),vtemp2d(1)) + call matvec2(Ug2der(1,1,i+2),dd(1,1,k+1),vtemp2d(1)) + s8d = -(atemp(1,1)+atemp(2,2))*scalar2(cc(1,1,l),vtemp2d(1)) #endif s12d = scalar2(Ub2der(1,i+2),vtemp3(1)) #ifdef MOMENT call matmat2(achuj_temp(1,1),EUgder(1,1,i+2),gtempd(1,1)) call matmat2(gtempd(1,1),EUg(1,1,i+3),gtempd(1,1)) s13d = (gtempd(1,1)+gtempd(2,2))*ss13 -#else - s13d=0.0d0 #endif c s1d=0.0d0 c s2d=0.0d0 @@ -7063,8 +8652,6 @@ C Derivatives in gamma(i+4) call matmat2(achuj_temp(1,1),EUg(1,1,i+2),gtempd(1,1)) call matmat2(gtempd(1,1),EUgder(1,1,i+3),gtempd(1,1)) s13d = (gtempd(1,1)+gtempd(2,2))*ss13 -#else - s13d = 0.0d0 #endif c s1d=0.0d0 c s2d=0.0d0 @@ -7081,27 +8668,21 @@ C Derivatives in gamma(i+5) call transpose2(AEAderg(1,1,1),auxmatd(1,1)) call matmat2(EUg(1,1,i+1),auxmatd(1,1),auxmatd(1,1)) s1d = (auxmatd(1,1)+auxmatd(2,2))*ss1 -#else - s1d = 0.0d0 #endif - call matvec2(EUg(1,1,i+2),b1(1,itl),vtemp1d(1)) + call matvec2(EUg(1,1,i+2),b1(1,l),vtemp1d(1)) call matvec2(AEAderg(1,1,1),vtemp1d(1),vtemp1d(1)) - s2d = scalar2(b1(1,itk),vtemp1d(1)) + s2d = scalar2(b1(1,k),vtemp1d(1)) #ifdef MOMENT call transpose2(AEA(1,1,2),atempd(1,1)) call matmat2(atempd(1,1),EUgder(1,1,i+4),atempd(1,1)) - s8d = -(atempd(1,1)+atempd(2,2))*scalar2(cc(1,1,itl),vtemp2(1)) -#else - s8d = 0.0d0 + s8d = -(atempd(1,1)+atempd(2,2))*scalar2(cc(1,1,l),vtemp2(1)) #endif call matvec2(auxmat(1,1),Ub2der(1,i+4),vtemp3d(1)) s12d = scalar2(Ub2(1,i+2),vtemp3d(1)) #ifdef MOMENT call matvec2(a_chuj(1,1,jj,i),Ub2der(1,i+4),vtemp4d(1)) - ss13d = scalar2(b1(1,itk),vtemp4d(1)) + ss13d = scalar2(b1(1,k),vtemp4d(1)) s13d = (gtemp(1,1)+gtemp(2,2))*ss13d -#else - s13d = 0.0d0 #endif c s1d=0.0d0 c s2d=0.0d0 @@ -7123,20 +8704,16 @@ C Cartesian derivatives call transpose2(AEAderx(1,1,lll,kkk,iii,1),auxmatd(1,1)) call matmat2(EUg(1,1,i+1),auxmatd(1,1),auxmatd(1,1)) s1d = (auxmatd(1,1)+auxmatd(2,2))*ss1 -#else - s1d = 0.0d0 #endif - call matvec2(EUg(1,1,i+2),b1(1,itl),vtemp1(1)) + call matvec2(EUg(1,1,i+2),b1(1,l),vtemp1(1)) call matvec2(AEAderx(1,1,lll,kkk,iii,1),vtemp1(1), & vtemp1d(1)) - s2d = scalar2(b1(1,itk),vtemp1d(1)) + s2d = scalar2(b1(1,k),vtemp1d(1)) #ifdef MOMENT call transpose2(AEAderx(1,1,lll,kkk,iii,2),atempd(1,1)) call matmat2(atempd(1,1),EUg(1,1,i+4),atempd(1,1)) s8d = -(atempd(1,1)+atempd(2,2))* - & scalar2(cc(1,1,itl),vtemp2(1)) -#else - s8d = 0.0d0 + & scalar2(cc(1,1,l),vtemp2(1)) #endif call matmat2(EUg(1,1,i+3),AEAderx(1,1,lll,kkk,iii,2), & auxmatd(1,1)) @@ -7175,7 +8752,7 @@ c s13d=0.0d0 derx_turn(lll,kkk,2) = derx_turn(lll,kkk,2)-0.5d0*s13d call matvec2(a_chuj_der(1,1,lll,kkk,jj,i),Ub2(1,i+4), & vtemp4d(1)) - ss13d = scalar2(b1(1,itk),vtemp4d(1)) + ss13d = scalar2(b1(1,k),vtemp4d(1)) s13d = (gtemp(1,1)+gtemp(2,2))*ss13d derx_turn(lll,kkk,1) = derx_turn(lll,kkk,1)-0.5d0*s13d enddo @@ -7199,57 +8776,183 @@ cd goto 1112 l2=l-2 endif do ll=1,3 - ggg1(ll)=eel_turn6*g_contij(ll,1) - ggg2(ll)=eel_turn6*g_contij(ll,2) - ghalf=0.5d0*ggg1(ll) +cgrad ggg1(ll)=eel_turn6*g_contij(ll,1) +cgrad ggg2(ll)=eel_turn6*g_contij(ll,2) +cgrad ghalf=0.5d0*ggg1(ll) cd ghalf=0.0d0 - gcorr6_turn(ll,i)=gcorr6_turn(ll,i)+ghalf + gturn6ij=eel_turn6*g_contij(ll,1)+ekont*derx_turn(ll,1,1) + gturn6kl=eel_turn6*g_contij(ll,2)+ekont*derx_turn(ll,1,2) + gcorr6_turn(ll,i)=gcorr6_turn(ll,i)!+ghalf & +ekont*derx_turn(ll,2,1) gcorr6_turn(ll,i+1)=gcorr6_turn(ll,i+1)+ekont*derx_turn(ll,3,1) - gcorr6_turn(ll,j)=gcorr6_turn(ll,j)+ghalf + gcorr6_turn(ll,j)=gcorr6_turn(ll,j)!+ghalf & +ekont*derx_turn(ll,4,1) gcorr6_turn(ll,j1)=gcorr6_turn(ll,j1)+ekont*derx_turn(ll,5,1) - ghalf=0.5d0*ggg2(ll) + gcorr6_turn_long(ll,j)=gcorr6_turn_long(ll,j)+gturn6ij + gcorr6_turn_long(ll,i)=gcorr6_turn_long(ll,i)-gturn6ij +cgrad ghalf=0.5d0*ggg2(ll) cd ghalf=0.0d0 - gcorr6_turn(ll,k)=gcorr6_turn(ll,k)+ghalf + gcorr6_turn(ll,k)=gcorr6_turn(ll,k)!+ghalf & +ekont*derx_turn(ll,2,2) gcorr6_turn(ll,k+1)=gcorr6_turn(ll,k+1)+ekont*derx_turn(ll,3,2) - gcorr6_turn(ll,l)=gcorr6_turn(ll,l)+ghalf + gcorr6_turn(ll,l)=gcorr6_turn(ll,l)!+ghalf & +ekont*derx_turn(ll,4,2) gcorr6_turn(ll,l1)=gcorr6_turn(ll,l1)+ekont*derx_turn(ll,5,2) + gcorr6_turn_long(ll,l)=gcorr6_turn_long(ll,l)+gturn6kl + gcorr6_turn_long(ll,k)=gcorr6_turn_long(ll,k)-gturn6kl enddo cd goto 1112 - do m=i+1,j-1 - do ll=1,3 - gcorr6_turn(ll,m)=gcorr6_turn(ll,m)+ggg1(ll) - enddo - enddo - do m=k+1,l-1 - do ll=1,3 - gcorr6_turn(ll,m)=gcorr6_turn(ll,m)+ggg2(ll) - enddo - enddo -1112 continue - do m=i+2,j2 - do ll=1,3 - gcorr6_turn(ll,m)=gcorr6_turn(ll,m)+ekont*derx_turn(ll,1,1) - enddo - enddo - do m=k+2,l2 - do ll=1,3 - gcorr6_turn(ll,m)=gcorr6_turn(ll,m)+ekont*derx_turn(ll,1,2) - enddo - enddo +cgrad do m=i+1,j-1 +cgrad do ll=1,3 +cgrad gcorr6_turn(ll,m)=gcorr6_turn(ll,m)+ggg1(ll) +cgrad enddo +cgrad enddo +cgrad do m=k+1,l-1 +cgrad do ll=1,3 +cgrad gcorr6_turn(ll,m)=gcorr6_turn(ll,m)+ggg2(ll) +cgrad enddo +cgrad enddo +cgrad1112 continue +cgrad do m=i+2,j2 +cgrad do ll=1,3 +cgrad gcorr6_turn(ll,m)=gcorr6_turn(ll,m)+ekont*derx_turn(ll,1,1) +cgrad enddo +cgrad enddo +cgrad do m=k+2,l2 +cgrad do ll=1,3 +cgrad gcorr6_turn(ll,m)=gcorr6_turn(ll,m)+ekont*derx_turn(ll,1,2) +cgrad enddo +cgrad enddo cd do iii=1,nres-3 cd write (2,*) iii,g_corr6_loc(iii) cd enddo - endif + endif ! calc_grad eello_turn6=ekont*eel_turn6 cd write (2,*) 'ekont',ekont cd write (2,*) 'eel_turn6',ekont*eel_turn6 return end + crc------------------------------------------------- +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC + subroutine Eliptransfer(eliptran) + implicit real*8 (a-h,o-z) + include 'DIMENSIONS' + include 'COMMON.GEO' + include 'COMMON.VAR' + include 'COMMON.LOCAL' + include 'COMMON.CHAIN' + include 'COMMON.DERIV' + include 'COMMON.INTERACT' + include 'COMMON.IOUNITS' + include 'COMMON.CALC' + include 'COMMON.CONTROL' + include 'COMMON.SPLITELE' + include 'COMMON.SBRIDGE' +C this is done by Adasko +C print *,"wchodze" +C structure of box: +C water +C--bordliptop-- buffore starts +C--bufliptop--- here true lipid starts +C lipid +C--buflipbot--- lipid ends buffore starts +C--bordlipbot--buffore ends + eliptran=0.0 + do i=1,nres +C do i=1,1 + if (itype(i).eq.ntyp1) cycle + + positi=(mod(((c(3,i)+c(3,i+1))/2.0d0),boxzsize)) + if (positi.le.0) positi=positi+boxzsize +C print *,i +C first for peptide groups +c for each residue check if it is in lipid or lipid water border area + if ((positi.gt.bordlipbot) + &.and.(positi.lt.bordliptop)) then +C the energy transfer exist + if (positi.lt.buflipbot) then +C what fraction I am in + fracinbuf=1.0d0- + & ((positi-bordlipbot)/lipbufthick) +C lipbufthick is thickenes of lipid buffore + sslip=sscalelip(fracinbuf) + ssgradlip=-sscagradlip(fracinbuf)/lipbufthick + eliptran=eliptran+sslip*pepliptran + gliptranc(3,i)=gliptranc(3,i)+ssgradlip*pepliptran/2.0d0 + gliptranc(3,i-1)=gliptranc(3,i-1)+ssgradlip*pepliptran/2.0d0 +C gliptranc(3,i-2)=gliptranc(3,i)+ssgradlip*pepliptran + elseif (positi.gt.bufliptop) then + fracinbuf=1.0d0-((bordliptop-positi)/lipbufthick) + sslip=sscalelip(fracinbuf) + ssgradlip=sscagradlip(fracinbuf)/lipbufthick + eliptran=eliptran+sslip*pepliptran + gliptranc(3,i)=gliptranc(3,i)+ssgradlip*pepliptran/2.0d0 + gliptranc(3,i-1)=gliptranc(3,i-1)+ssgradlip*pepliptran/2.0d0 +C gliptranc(3,i-2)=gliptranc(3,i)+ssgradlip*pepliptran +C print *, "doing sscalefor top part" +C print *,i,sslip,fracinbuf,ssgradlip + else + eliptran=eliptran+pepliptran +C print *,"I am in true lipid" + endif +C else +C eliptran=elpitran+0.0 ! I am in water + endif + enddo +C print *, "nic nie bylo w lipidzie?" +C now multiply all by the peptide group transfer factor +C eliptran=eliptran*pepliptran +C now the same for side chains +CV do i=1,1 + do i=1,nres + if (itype(i).eq.ntyp1) cycle + positi=(mod(c(3,i+nres),boxzsize)) + if (positi.le.0) positi=positi+boxzsize +C print *,mod(c(3,i+nres),boxzsize),bordlipbot,bordliptop +c for each residue check if it is in lipid or lipid water border area +C respos=mod(c(3,i+nres),boxzsize) +C print *,positi,bordlipbot,buflipbot + if ((positi.gt.bordlipbot) + & .and.(positi.lt.bordliptop)) then +C the energy transfer exist + if (positi.lt.buflipbot) then + fracinbuf=1.0d0- + & ((positi-bordlipbot)/lipbufthick) +C lipbufthick is thickenes of lipid buffore + sslip=sscalelip(fracinbuf) + ssgradlip=-sscagradlip(fracinbuf)/lipbufthick + eliptran=eliptran+sslip*liptranene(itype(i)) + gliptranx(3,i)=gliptranx(3,i) + &+ssgradlip*liptranene(itype(i)) + gliptranc(3,i-1)= gliptranc(3,i-1) + &+ssgradlip*liptranene(itype(i)) +C print *,"doing sccale for lower part" + elseif (positi.gt.bufliptop) then + fracinbuf=1.0d0- + &((bordliptop-positi)/lipbufthick) + sslip=sscalelip(fracinbuf) + ssgradlip=sscagradlip(fracinbuf)/lipbufthick + eliptran=eliptran+sslip*liptranene(itype(i)) + gliptranx(3,i)=gliptranx(3,i) + &+ssgradlip*liptranene(itype(i)) + gliptranc(3,i-1)= gliptranc(3,i-1) + &+ssgradlip*liptranene(itype(i)) +C print *, "doing sscalefor top part",sslip,fracinbuf + else + eliptran=eliptran+liptranene(itype(i)) +C print *,"I am in true lipid" + endif + endif ! if in lipid or buffor +C else +C eliptran=elpitran+0.0 ! I am in water + enddo + return + end + + +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC + SUBROUTINE MATVEC2(A1,V1,V2) implicit real*8 (a-h,o-z) include 'DIMENSIONS' @@ -7383,4 +9086,443 @@ C----------------------------------------------------------------------------- scalar=sc return end +C----------------------------------------------------------------------- + double precision function sscale(r) + double precision r,gamm + include "COMMON.SPLITELE" + if(r.lt.r_cut-rlamb) then + sscale=1.0d0 + else if(r.le.r_cut.and.r.ge.r_cut-rlamb) then + gamm=(r-(r_cut-rlamb))/rlamb + sscale=1.0d0+gamm*gamm*(2*gamm-3.0d0) + else + sscale=0d0 + endif + return + end +C----------------------------------------------------------------------- +C----------------------------------------------------------------------- + double precision function sscagrad(r) + double precision r,gamm + include "COMMON.SPLITELE" + if(r.lt.r_cut-rlamb) then + sscagrad=0.0d0 + else if(r.le.r_cut.and.r.ge.r_cut-rlamb) then + gamm=(r-(r_cut-rlamb))/rlamb + sscagrad=gamm*(6*gamm-6.0d0)/rlamb + else + sscagrad=0.0d0 + endif + return + end +C----------------------------------------------------------------------- +C----------------------------------------------------------------------- + double precision function sscalelip(r) + double precision r,gamm + include "COMMON.SPLITELE" +C if(r.lt.r_cut-rlamb) then +C sscale=1.0d0 +C else if(r.le.r_cut.and.r.ge.r_cut-rlamb) then +C gamm=(r-(r_cut-rlamb))/rlamb + sscalelip=1.0d0+r*r*(2*r-3.0d0) +C else +C sscale=0d0 +C endif + return + end +C----------------------------------------------------------------------- + double precision function sscagradlip(r) + double precision r,gamm + include "COMMON.SPLITELE" +C if(r.lt.r_cut-rlamb) then +C sscagrad=0.0d0 +C else if(r.le.r_cut.and.r.ge.r_cut-rlamb) then +C gamm=(r-(r_cut-rlamb))/rlamb + sscagradlip=r*(6*r-6.0d0) +C else +C sscagrad=0.0d0 +C endif + return + end + +C----------------------------------------------------------------------- + subroutine set_shield_fac + implicit real*8 (a-h,o-z) + include 'DIMENSIONS' + include 'COMMON.CHAIN' + include 'COMMON.DERIV' + include 'COMMON.IOUNITS' + include 'COMMON.SHIELD' + include 'COMMON.INTERACT' +C this is the squar root 77 devided by 81 the epislion in lipid (in protein) + double precision div77_81/0.974996043d0/, + &div4_81/0.2222222222d0/,sh_frac_dist_grad(3) + +C the vector between center of side_chain and peptide group + double precision pep_side(3),long,side_calf(3), + &pept_group(3),costhet_grad(3),cosphi_grad_long(3), + &cosphi_grad_loc(3),pep_side_norm(3),side_calf_norm(3) +C the line belowe needs to be changed for FGPROC>1 + do i=1,nres-1 + if ((itype(i).eq.ntyp1).and.itype(i+1).eq.ntyp1) cycle + ishield_list(i)=0 +Cif there two consequtive dummy atoms there is no peptide group between them +C the line below has to be changed for FGPROC>1 + VolumeTotal=0.0 + do k=1,nres + if ((itype(k).eq.ntyp1).or.(itype(k).eq.10)) cycle + dist_pep_side=0.0 + dist_side_calf=0.0 + do j=1,3 +C first lets set vector conecting the ithe side-chain with kth side-chain + pep_side(j)=c(j,k+nres)-(c(j,i)+c(j,i+1))/2.0d0 +C pep_side(j)=2.0d0 +C and vector conecting the side-chain with its proper calfa + side_calf(j)=c(j,k+nres)-c(j,k) +C side_calf(j)=2.0d0 + pept_group(j)=c(j,i)-c(j,i+1) +C lets have their lenght + dist_pep_side=pep_side(j)**2+dist_pep_side + dist_side_calf=dist_side_calf+side_calf(j)**2 + dist_pept_group=dist_pept_group+pept_group(j)**2 + enddo + dist_pep_side=dsqrt(dist_pep_side) + dist_pept_group=dsqrt(dist_pept_group) + dist_side_calf=dsqrt(dist_side_calf) + do j=1,3 + pep_side_norm(j)=pep_side(j)/dist_pep_side + side_calf_norm(j)=dist_side_calf + enddo +C now sscale fraction + sh_frac_dist=-(dist_pep_side-rpp(1,1)-buff_shield)/buff_shield +C print *,buff_shield,"buff" +C now sscale + if (sh_frac_dist.le.0.0) cycle +C If we reach here it means that this side chain reaches the shielding sphere +C Lets add him to the list for gradient + ishield_list(i)=ishield_list(i)+1 +C ishield_list is a list of non 0 side-chain that contribute to factor gradient +C this list is essential otherwise problem would be O3 + shield_list(ishield_list(i),i)=k +C Lets have the sscale value + if (sh_frac_dist.gt.1.0) then + scale_fac_dist=1.0d0 + do j=1,3 + sh_frac_dist_grad(j)=0.0d0 + enddo + else + scale_fac_dist=-sh_frac_dist*sh_frac_dist + & *(2.0*sh_frac_dist-3.0d0) + fac_help_scale=6.0*(sh_frac_dist-sh_frac_dist**2) + & /dist_pep_side/buff_shield*0.5 +C remember for the final gradient multiply sh_frac_dist_grad(j) +C for side_chain by factor -2 ! + do j=1,3 + sh_frac_dist_grad(j)=fac_help_scale*pep_side(j) +C print *,"jestem",scale_fac_dist,fac_help_scale, +C & sh_frac_dist_grad(j) + enddo + endif +C if ((i.eq.3).and.(k.eq.2)) then +C print *,i,sh_frac_dist,dist_pep,fac_help_scale,scale_fac_dist +C & ,"TU" +C endif + +C this is what is now we have the distance scaling now volume... + short=short_r_sidechain(itype(k)) + long=long_r_sidechain(itype(k)) + costhet=1.0d0/dsqrt(1.0+short**2/dist_pep_side**2) +C now costhet_grad +C costhet=0.0d0 + costhet_fac=costhet**3*short**2*(-0.5)/dist_pep_side**4 +C costhet_fac=0.0d0 + do j=1,3 + costhet_grad(j)=costhet_fac*pep_side(j) + enddo +C remember for the final gradient multiply costhet_grad(j) +C for side_chain by factor -2 ! +C fac alfa is angle between CB_k,CA_k, CA_i,CA_i+1 +C pep_side0pept_group is vector multiplication + pep_side0pept_group=0.0 + do j=1,3 + pep_side0pept_group=pep_side0pept_group+pep_side(j)*side_calf(j) + enddo + cosalfa=(pep_side0pept_group/ + & (dist_pep_side*dist_side_calf)) + fac_alfa_sin=1.0-cosalfa**2 + fac_alfa_sin=dsqrt(fac_alfa_sin) + rkprim=fac_alfa_sin*(long-short)+short +C now costhet_grad + cosphi=1.0d0/dsqrt(1.0+rkprim**2/dist_pep_side**2) + cosphi_fac=cosphi**3*rkprim**2*(-0.5)/dist_pep_side**4 + + do j=1,3 + cosphi_grad_long(j)=cosphi_fac*pep_side(j) + &+cosphi**3*0.5/dist_pep_side**2*(-rkprim) + &*(long-short)/fac_alfa_sin*cosalfa/ + &((dist_pep_side*dist_side_calf))* + &((side_calf(j))-cosalfa* + &((pep_side(j)/dist_pep_side)*dist_side_calf)) + + cosphi_grad_loc(j)=cosphi**3*0.5/dist_pep_side**2*(-rkprim) + &*(long-short)/fac_alfa_sin*cosalfa + &/((dist_pep_side*dist_side_calf))* + &(pep_side(j)- + &cosalfa*side_calf(j)/dist_side_calf*dist_pep_side) + enddo + + VofOverlap=VSolvSphere/2.0d0*(1.0-costhet)*(1.0-cosphi) + & /VSolvSphere_div + & *wshield +C now the gradient... +C grad_shield is gradient of Calfa for peptide groups +C write(iout,*) "shield_compon",i,k,VSolvSphere,scale_fac_dist, +C & costhet,cosphi +C write(iout,*) "cosphi_compon",i,k,pep_side0pept_group, +C & dist_pep_side,dist_side_calf,c(1,k+nres),c(1,k),itype(k) + do j=1,3 + grad_shield(j,i)=grad_shield(j,i) +C gradient po skalowaniu + & +(sh_frac_dist_grad(j) +C gradient po costhet + &-scale_fac_dist*costhet_grad(j)/(1.0-costhet) + &-scale_fac_dist*(cosphi_grad_long(j)) + &/(1.0-cosphi) )*div77_81 + &*VofOverlap +C grad_shield_side is Cbeta sidechain gradient + grad_shield_side(j,ishield_list(i),i)= + & (sh_frac_dist_grad(j)*(-2.0d0) + & +scale_fac_dist*costhet_grad(j)*2.0d0/(1.0-costhet) + & +scale_fac_dist*(cosphi_grad_long(j)) + & *2.0d0/(1.0-cosphi)) + & *div77_81*VofOverlap + + grad_shield_loc(j,ishield_list(i),i)= + & scale_fac_dist*cosphi_grad_loc(j) + & *2.0d0/(1.0-cosphi) + & *div77_81*VofOverlap + enddo + VolumeTotal=VolumeTotal+VofOverlap*scale_fac_dist + enddo + fac_shield(i)=VolumeTotal*div77_81+div4_81 +C write(2,*) "TOTAL VOLUME",i,VolumeTotal,fac_shield(i) + enddo + return + end +C-------------------------------------------------------------------------- +C first for shielding is setting of function of side-chains + subroutine set_shield_fac2 + implicit real*8 (a-h,o-z) + include 'DIMENSIONS' + include 'COMMON.CHAIN' + include 'COMMON.DERIV' + include 'COMMON.IOUNITS' + include 'COMMON.SHIELD' + include 'COMMON.INTERACT' +C this is the squar root 77 devided by 81 the epislion in lipid (in protein) + double precision div77_81/0.974996043d0/, + &div4_81/0.2222222222d0/,sh_frac_dist_grad(3) + +C the vector between center of side_chain and peptide group + double precision pep_side(3),long,side_calf(3), + &pept_group(3),costhet_grad(3),cosphi_grad_long(3), + &cosphi_grad_loc(3),pep_side_norm(3),side_calf_norm(3) +C the line belowe needs to be changed for FGPROC>1 + do i=1,nres-1 + if ((itype(i).eq.ntyp1).and.itype(i+1).eq.ntyp1) cycle + ishield_list(i)=0 +Cif there two consequtive dummy atoms there is no peptide group between them +C the line below has to be changed for FGPROC>1 + VolumeTotal=0.0 + do k=1,nres + if ((itype(k).eq.ntyp1).or.(itype(k).eq.10)) cycle + dist_pep_side=0.0 + dist_side_calf=0.0 + do j=1,3 +C first lets set vector conecting the ithe side-chain with kth side-chain + pep_side(j)=c(j,k+nres)-(c(j,i)+c(j,i+1))/2.0d0 +C pep_side(j)=2.0d0 +C and vector conecting the side-chain with its proper calfa + side_calf(j)=c(j,k+nres)-c(j,k) +C side_calf(j)=2.0d0 + pept_group(j)=c(j,i)-c(j,i+1) +C lets have their lenght + dist_pep_side=pep_side(j)**2+dist_pep_side + dist_side_calf=dist_side_calf+side_calf(j)**2 + dist_pept_group=dist_pept_group+pept_group(j)**2 + enddo + dist_pep_side=dsqrt(dist_pep_side) + dist_pept_group=dsqrt(dist_pept_group) + dist_side_calf=dsqrt(dist_side_calf) + do j=1,3 + pep_side_norm(j)=pep_side(j)/dist_pep_side + side_calf_norm(j)=dist_side_calf + enddo +C now sscale fraction + sh_frac_dist=-(dist_pep_side-rpp(1,1)-buff_shield)/buff_shield +C print *,buff_shield,"buff" +C now sscale + if (sh_frac_dist.le.0.0) cycle +C If we reach here it means that this side chain reaches the shielding sphere +C Lets add him to the list for gradient + ishield_list(i)=ishield_list(i)+1 +C ishield_list is a list of non 0 side-chain that contribute to factor gradient +C this list is essential otherwise problem would be O3 + shield_list(ishield_list(i),i)=k +C Lets have the sscale value + if (sh_frac_dist.gt.1.0) then + scale_fac_dist=1.0d0 + do j=1,3 + sh_frac_dist_grad(j)=0.0d0 + enddo + else + scale_fac_dist=-sh_frac_dist*sh_frac_dist + & *(2.0d0*sh_frac_dist-3.0d0) + fac_help_scale=6.0d0*(sh_frac_dist-sh_frac_dist**2) + & /dist_pep_side/buff_shield*0.5d0 +C remember for the final gradient multiply sh_frac_dist_grad(j) +C for side_chain by factor -2 ! + do j=1,3 + sh_frac_dist_grad(j)=fac_help_scale*pep_side(j) +C sh_frac_dist_grad(j)=0.0d0 +C scale_fac_dist=1.0d0 +C print *,"jestem",scale_fac_dist,fac_help_scale, +C & sh_frac_dist_grad(j) + enddo + endif +C this is what is now we have the distance scaling now volume... + short=short_r_sidechain(itype(k)) + long=long_r_sidechain(itype(k)) + costhet=1.0d0/dsqrt(1.0d0+short**2/dist_pep_side**2) + sinthet=short/dist_pep_side*costhet +C now costhet_grad +C costhet=0.6d0 +C sinthet=0.8 + costhet_fac=costhet**3*short**2*(-0.5d0)/dist_pep_side**4 +C sinthet_fac=costhet**2*0.5d0*(short**3/dist_pep_side**4*costhet +C & -short/dist_pep_side**2/costhet) +C costhet_fac=0.0d0 + do j=1,3 + costhet_grad(j)=costhet_fac*pep_side(j) + enddo +C remember for the final gradient multiply costhet_grad(j) +C for side_chain by factor -2 ! +C fac alfa is angle between CB_k,CA_k, CA_i,CA_i+1 +C pep_side0pept_group is vector multiplication + pep_side0pept_group=0.0d0 + do j=1,3 + pep_side0pept_group=pep_side0pept_group+pep_side(j)*side_calf(j) + enddo + cosalfa=(pep_side0pept_group/ + & (dist_pep_side*dist_side_calf)) + fac_alfa_sin=1.0d0-cosalfa**2 + fac_alfa_sin=dsqrt(fac_alfa_sin) + rkprim=fac_alfa_sin*(long-short)+short +C rkprim=short + +C now costhet_grad + cosphi=1.0d0/dsqrt(1.0d0+rkprim**2/dist_pep_side**2) +C cosphi=0.6 + cosphi_fac=cosphi**3*rkprim**2*(-0.5d0)/dist_pep_side**4 + sinphi=rkprim/dist_pep_side/dsqrt(1.0d0+rkprim**2/ + & dist_pep_side**2) +C sinphi=0.8 + do j=1,3 + cosphi_grad_long(j)=cosphi_fac*pep_side(j) + &+cosphi**3*0.5d0/dist_pep_side**2*(-rkprim) + &*(long-short)/fac_alfa_sin*cosalfa/ + &((dist_pep_side*dist_side_calf))* + &((side_calf(j))-cosalfa* + &((pep_side(j)/dist_pep_side)*dist_side_calf)) +C cosphi_grad_long(j)=0.0d0 + cosphi_grad_loc(j)=cosphi**3*0.5d0/dist_pep_side**2*(-rkprim) + &*(long-short)/fac_alfa_sin*cosalfa + &/((dist_pep_side*dist_side_calf))* + &(pep_side(j)- + &cosalfa*side_calf(j)/dist_side_calf*dist_pep_side) +C cosphi_grad_loc(j)=0.0d0 + enddo +C print *,sinphi,sinthet + VofOverlap=VSolvSphere/2.0d0*(1.0d0-dsqrt(1.0d0-sinphi*sinthet)) + & /VSolvSphere_div +C & *wshield +C now the gradient... + do j=1,3 + grad_shield(j,i)=grad_shield(j,i) +C gradient po skalowaniu + & +(sh_frac_dist_grad(j)*VofOverlap +C gradient po costhet + & +scale_fac_dist*VSolvSphere/VSolvSphere_div/4.0d0* + &(1.0d0/(-dsqrt(1.0d0-sinphi*sinthet))*( + & sinphi/sinthet*costhet*costhet_grad(j) + & +sinthet/sinphi*cosphi*cosphi_grad_long(j))) + & )*wshield +C grad_shield_side is Cbeta sidechain gradient + grad_shield_side(j,ishield_list(i),i)= + & (sh_frac_dist_grad(j)*(-2.0d0) + & *VofOverlap + & -scale_fac_dist*VSolvSphere/VSolvSphere_div/2.0d0* + &(1.0d0/(-dsqrt(1.0d0-sinphi*sinthet))*( + & sinphi/sinthet*costhet*costhet_grad(j) + & +sinthet/sinphi*cosphi*cosphi_grad_long(j))) + & )*wshield + + grad_shield_loc(j,ishield_list(i),i)= + & scale_fac_dist*VSolvSphere/VSolvSphere_div/2.0d0* + &(1.0d0/(dsqrt(1.0d0-sinphi*sinthet))*( + & sinthet/sinphi*cosphi*cosphi_grad_loc(j) + & )) + & *wshield + enddo + VolumeTotal=VolumeTotal+VofOverlap*scale_fac_dist + enddo + fac_shield(i)=VolumeTotal*wshield+(1.0d0-wshield) +C write(2,*) "TOTAL VOLUME",i,VolumeTotal,fac_shield(i) +C write(2,*) "TU",rpp(1,1),short,long,buff_shield + enddo + return + end +C-------------------------------------------------------------------------- + double precision function tschebyshev(m,n,x,y) + implicit none + include "DIMENSIONS" + integer i,m,n + double precision x(n),y,yy(0:maxvar),aux +c Tschebyshev polynomial. Note that the first term is omitted +c m=0: the constant term is included +c m=1: the constant term is not included + yy(0)=1.0d0 + yy(1)=y + do i=2,n + yy(i)=2*yy(1)*yy(i-1)-yy(i-2) + enddo + aux=0.0d0 + do i=m,n + aux=aux+x(i)*yy(i) + enddo + tschebyshev=aux + return + end +C-------------------------------------------------------------------------- + double precision function gradtschebyshev(m,n,x,y) + implicit none + include "DIMENSIONS" + integer i,m,n + double precision x(n+1),y,yy(0:maxvar),aux +c Tschebyshev polynomial. Note that the first term is omitted +c m=0: the constant term is included +c m=1: the constant term is not included + yy(0)=1.0d0 + yy(1)=2.0d0*y + do i=2,n + yy(i)=2*y*yy(i-1)-yy(i-2) + enddo + aux=0.0d0 + do i=m,n + aux=aux+x(i+1)*yy(i)*(i+1) +C print *, x(i+1),yy(i),i + enddo + gradtschebyshev=aux + return + end