X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fsrc_MD-M%2Fenergy_p_new_barrier.F;h=e3a17dd1d69b8645e431f6d8003e0c3c5bda09f5;hb=46f3f544d5a60812e2e11e03b619903f2ed052eb;hp=109af351c026cf52a7ab4975e320166eb0a54e1d;hpb=7ac044004baeac41c3c91c38a1b3c3546287e624;p=unres.git diff --git a/source/unres/src_MD-M/energy_p_new_barrier.F b/source/unres/src_MD-M/energy_p_new_barrier.F index 109af35..e3a17dd 100644 --- a/source/unres/src_MD-M/energy_p_new_barrier.F +++ b/source/unres/src_MD-M/energy_p_new_barrier.F @@ -10,6 +10,8 @@ cMS$ATTRIBUTES C :: proc_proc #ifdef MPI include "mpif.h" double precision weights_(n_ene) + integer IERR + integer status(MPI_STATUS_SIZE) #endif include 'COMMON.SETUP' include 'COMMON.IOUNITS' @@ -25,6 +27,13 @@ cMS$ATTRIBUTES C :: proc_proc include 'COMMON.CONTROL' include 'COMMON.TIME1' include 'COMMON.SPLITELE' + include 'COMMON.SHIELD' + double precision fac_shieldbuf(maxres), + & grad_shield_locbuf(3,maxcontsshi,-1:maxres), + & grad_shield_sidebuf(3,maxcontsshi,-1:maxres), + & grad_shieldbuf(3,-1:maxres) + integer ishield_listbuf(maxres), + &shield_listbuf(maxcontsshi,maxres) #ifdef MPI c print*,"ETOTAL Processor",fg_rank," absolute rank",myrank, c & " nfgtasks",nfgtasks @@ -55,6 +64,8 @@ C FG slaves as WEIGHTS array. weights_(17)=wbond weights_(18)=scal14 weights_(21)=wsccor + weights_(22)=wtube + C FG Master broadcasts the WEIGHTS_ array call MPI_Bcast(weights_(1),n_ene, & MPI_DOUBLE_PRECISION,king,FG_COMM,IERROR) @@ -81,6 +92,7 @@ C FG slaves receive the WEIGHTS array wbond=weights(17) scal14=weights(18) wsccor=weights(21) + wtube=weights(22) endif time_Bcast=time_Bcast+MPI_Wtime()-time00 time_Bcastw=time_Bcastw+MPI_Wtime()-time00 @@ -141,9 +153,84 @@ C Introduction of shielding effect first for each peptide group C the shielding factor is set this factor is describing how each C peptide group is shielded by side-chains C the matrix - shield_fac(i) the i index describe the ith between i and i+1 - write (iout,*) "shield_mode",shield_mode - if (shield_mode.gt.0) then +C write (iout,*) "shield_mode",shield_mode + if (shield_mode.eq.1) then call set_shield_fac + else if (shield_mode.eq.2) then + call set_shield_fac2 + if (nfgtasks.gt.1) then +C#define DEBUG +#ifdef DEBUG + write(iout,*) "befor reduce fac_shield reduce" + do i=1,nres + write(2,*) "fac",itype(i),fac_shield(i),grad_shield(1,i) + write(2,*) "list", shield_list(1,i),ishield_list(i), + & grad_shield_side(1,1,i),grad_shield_loc(1,1,i) + enddo +#endif + call MPI_Allgatherv(fac_shield(ivec_start), + & ivec_count(fg_rank1), + & MPI_DOUBLE_PRECISION,fac_shieldbuf(1),ivec_count(0), + & ivec_displ(0), + & MPI_DOUBLE_PRECISION,FG_COMM,IERR) + call MPI_Allgatherv(shield_list(1,ivec_start), + & ivec_count(fg_rank1), + & MPI_I50,shield_listbuf(1,1),ivec_count(0), + & ivec_displ(0), + & MPI_I50,FG_COMM,IERR) + call MPI_Allgatherv(ishield_list(ivec_start), + & ivec_count(fg_rank1), + & MPI_INTEGER,ishield_listbuf(1),ivec_count(0), + & ivec_displ(0), + & MPI_INTEGER,FG_COMM,IERR) + call MPI_Allgatherv(grad_shield(1,ivec_start), + & ivec_count(fg_rank1), + & MPI_UYZ,grad_shieldbuf(1,1),ivec_count(0), + & ivec_displ(0), + & MPI_UYZ,FG_COMM,IERR) + call MPI_Allgatherv(grad_shield_side(1,1,ivec_start), + & ivec_count(fg_rank1), + & MPI_SHI,grad_shield_sidebuf(1,1,1),ivec_count(0), + & ivec_displ(0), + & MPI_SHI,FG_COMM,IERR) + call MPI_Allgatherv(grad_shield_loc(1,1,ivec_start), + & ivec_count(fg_rank1), + & MPI_SHI,grad_shield_locbuf(1,1,1),ivec_count(0), + & ivec_displ(0), + & MPI_SHI,FG_COMM,IERR) + do i=1,nres + fac_shield(i)=fac_shieldbuf(i) + ishield_list(i)=ishield_listbuf(i) + do j=1,3 + grad_shield(j,i)=grad_shieldbuf(j,i) + enddo !j + do j=1,ishield_list(i) + shield_list(j,i)=shield_listbuf(j,i) + do k=1,3 + grad_shield_loc(k,j,i)=grad_shield_locbuf(k,j,i) + grad_shield_side(k,j,i)=grad_shield_sidebuf(k,j,i) + enddo !k + enddo !j + enddo !i +#ifdef DEBUG + write(iout,*) "after reduce fac_shield reduce" + do i=1,nres + write(2,*) "fac",itype(i),fac_shield(i),grad_shield(1,i) + write(2,*) "list", shield_list(1,i),ishield_list(i), + & grad_shield_side(1,1,i),grad_shield_loc(1,1,i) + enddo +#endif +C#undef DEBUG + endif +#ifdef DEBUG + do i=1,nres + write(iout,*) fac_shield(i),ishield_list(i),i,grad_shield(1,i) + do j=1,ishield_list(i) + write(iout,*) "grad", grad_shield_side(1,j,i), + & grad_shield_loc(1,j,i) + enddo + enddo +#endif endif c print *,"Processor",myrank," left VEC_AND_DERIV" if (ipot.lt.6) then @@ -201,7 +288,14 @@ C C Calculate the virtual-bond-angle energy. C if (wang.gt.0d0) then + if ((tor_mode.eq.0).or.(tor_mode.eq.2)) then call ebend(ebe,ethetacnstr) + endif +C ebend kcc is Kubo cumulant clustered rigorous attemp to derive the +C energy function + if ((tor_mode.eq.1).or.(tor_mode.eq.2)) then + call ebend_kcc(ebe,ethetacnstr) + endif else ebe=0 ethetacnstr=0 @@ -217,8 +311,16 @@ C C Calculate the virtual-bond torsional energy. C cd print *,'nterm=',nterm +C print *,"tor",tor_mode if (wtor.gt.0) then + if ((tor_mode.eq.0).or.(tor_mode.eq.2)) then call etor(etors,edihcnstr) + endif +C etor kcc is Kubo cumulant clustered rigorous attemp to derive the +C energy function + if ((tor_mode.eq.1).or.(tor_mode.eq.2)) then + call etor_kcc(etors,edihcnstr) + endif else etors=0 edihcnstr=0 @@ -227,7 +329,7 @@ c print *,"Processor",myrank," computed Utor" C C 6/23/01 Calculate double-torsional energy C - if (wtor_d.gt.0) then + if ((wtor_d.gt.0).and.((tor_mode.eq.0).or.(tor_mode.eq.2))) then call etor_d(etors_d) else etors_d=0 @@ -280,6 +382,8 @@ C based on partition function C print *,"przed lipidami" if (wliptran.gt.0) then call Eliptransfer(eliptran) + else + eliptran=0.0d0 endif C print *,"za lipidami" if (AFMlog.gt.0) then @@ -287,6 +391,17 @@ C print *,"za lipidami" else if (selfguide.gt.0) then call AFMvel(Eafmforce) endif + if (TUBElog.eq.1) then +C print *,"just before call" + call calctube(Etube) + elseif (TUBElog.eq.2) then + call calctube2(Etube) + elseif (TUBElog.eq.3) then + call calcnano(Etube) + else + Etube=0.0d0 + endif + #ifdef TIMING time_enecalc=time_enecalc+MPI_Wtime()-time00 #endif @@ -331,6 +446,7 @@ C energia(22)=eliptran energia(23)=Eafmforce energia(24)=ethetacnstr + energia(25)=Etube c Here are the energies showed per procesor if the are more processors c per molecule then we sum it up in sum_energy subroutine c print *," Processor",myrank," calls SUM_ENERGY" @@ -425,6 +541,7 @@ cMS$ATTRIBUTES C :: proc_proc eliptran=energia(22) Eafmforce=energia(23) ethetacnstr=energia(24) + Etube=energia(25) #ifdef SPLITELE etot=wsc*evdw+wscp*evdw2+welec*ees+wvdwpp*evdw1 & +wang*ebe+wtor*etors+wscloc*escloc @@ -432,7 +549,7 @@ cMS$ATTRIBUTES C :: proc_proc & +wcorr6*ecorr6+wturn4*eello_turn4+wturn3*eello_turn3 & +wturn6*eturn6+wel_loc*eel_loc+edihcnstr+wtor_d*etors_d & +wbond*estr+Uconst+wsccor*esccor+wliptran*eliptran+Eafmforce - & +ethetacnstr + & +ethetacnstr+wtube*Etube #else etot=wsc*evdw+wscp*evdw2+welec*(ees+evdw1) & +wang*ebe+wtor*etors+wscloc*escloc @@ -441,7 +558,7 @@ cMS$ATTRIBUTES C :: proc_proc & +wturn6*eturn6+wel_loc*eel_loc+edihcnstr+wtor_d*etors_d & +wbond*estr+Uconst+wsccor*esccor+wliptran*eliptran & +Eafmforce - & +ethetacnstr + & +ethetacnstr+wtube*Etube #endif energia(0)=etot c detecting NaNQ @@ -546,9 +663,36 @@ c enddo & wstrain*ghpbc(j,i) & +wliptran*gliptranc(j,i) & +gradafm(j,i) + & +welec*gshieldc(j,i) + & +wcorr*gshieldc_ec(j,i) + & +wturn3*gshieldc_t3(j,i) + & +wturn4*gshieldc_t4(j,i) + & +wel_loc*gshieldc_ll(j,i) + & +wtube*gg_tube(j,i) + + enddo - enddo + enddo +C j=1 +C i=0 +C print *,"KUPA2",gradbufc(j,i),wsc*gvdwc(j,i), +C & wscp*gvdwc_scp(j,i),gvdwc_scpp(j,i), +C & welec*gelc_long(j,i),wvdwpp*gvdwpp(j,i), +C & wel_loc*gel_loc_long(j,i), +C & wcorr*gradcorr_long(j,i), +C & wcorr5*gradcorr5_long(j,i), +C & wcorr6*gradcorr6_long(j,i), +C & wturn6*gcorr6_turn_long(j,i), +C & wstrain*ghpbc(j,i) +C & ,wliptran*gliptranc(j,i) +C & ,gradafm(j,i) +C & ,welec*gshieldc(j,i) +C & ,wcorr*gshieldc_ec(j,i) +C & ,wturn3*gshieldc_t3(j,i) +C & ,wturn4*gshieldc_t4(j,i) +C & ,wel_loc*gshieldc_ll(j,i) +C & ,wtube*gg_tube(j,i) #else do i=0,nct do j=1,3 @@ -564,6 +708,13 @@ c enddo & wstrain*ghpbc(j,i) & +wliptran*gliptranc(j,i) & +gradafm(j,i) + & +welec*gshieldc(j,i) + & +wcorr*gshieldc_ec(j,i) + & +wturn4*gshieldc_t4(j,i) + & +wel_loc*gshieldc_ll(j,i) + & +wtube*gg_tube(j,i) + + enddo enddo @@ -596,7 +747,7 @@ c call flush(iout) #ifdef TIMING c time_allreduce=time_allreduce+MPI_Wtime()-time00 #endif - do i=nnt,nres + do i=0,nres do k=1,3 gradbufc(k,i)=0.0d0 enddo @@ -682,6 +833,13 @@ c enddo do i=-1,nct do j=1,3 #ifdef SPLITELE +C print *,gradbufc(1,13) +C print *,welec*gelc(1,13) +C print *,wel_loc*gel_loc(1,13) +C print *,0.5d0*(wscp*gvdwc_scpp(1,13)) +C print *,welec*gelc_long(1,13)+wvdwpp*gvdwpp(1,13) +C print *,wel_loc*gel_loc_long(1,13) +C print *,gradafm(1,13),"AFM" gradc(j,i,icg)=gradbufc(j,i)+welec*gelc(j,i)+ & wel_loc*gel_loc(j,i)+ & 0.5d0*(wscp*gvdwc_scpp(j,i)+ @@ -702,11 +860,23 @@ c enddo & +wscloc*gscloc(j,i) & +wliptran*gliptranc(j,i) & +gradafm(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) + & +wtube*gg_tube(j,i) + #else gradc(j,i,icg)=gradbufc(j,i)+welec*gelc(j,i)+ & wel_loc*gel_loc(j,i)+ & 0.5d0*(wscp*gvdwc_scpp(j,i)+ - & welec*gelc_long(j,i) + & welec*gelc_long(j,i)+ & wel_loc*gel_loc_long(j,i)+ & wcorr*gcorr_long(j,i)+ & wcorr5*gradcorr5_long(j,i)+ @@ -723,6 +893,18 @@ c enddo & +wscloc*gscloc(j,i) & +wliptran*gliptranc(j,i) & +gradafm(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) + & +wtube*gg_tube(j,i) + #endif gradx(j,i,icg)=wsc*gvdwx(j,i)+wscp*gradx_scp(j,i)+ @@ -731,8 +913,52 @@ c enddo & wsccor*gsccorx(j,i) & +wscloc*gsclocx(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) + & +wtube*gg_tube_sc(j,i) + + + enddo - enddo + enddo +C i=0 +C j=1 +C print *,"KUPA", gradbufc(j,i),welec*gelc(j,i), +C & wel_loc*gel_loc(j,i), +C & 0.5d0*wscp*gvdwc_scpp(j,i), +C & welec*gelc_long(j,i),wvdwpp*gvdwpp(j,i), +C & wel_loc*gel_loc_long(j,i), +C & wcorr*gradcorr_long(j,i), +C & wcorr5*gradcorr5_long(j,i), +C & wcorr6*gradcorr6_long(j,i), +C & wturn6*gcorr6_turn_long(j,i), +C & wbond*gradb(j,i), +C & wcorr*gradcorr(j,i), +C & wturn3*gcorr3_turn(j,i), +C & wturn4*gcorr4_turn(j,i), +C & wcorr5*gradcorr5(j,i), +C & wcorr6*gradcorr6(j,i), +C & wturn6*gcorr6_turn(j,i), +C & wsccor*gsccorc(j,i) +C & ,wscloc*gscloc(j,i) +C & ,wliptran*gliptranc(j,i) +C & ,gradafm(j,i) +C & +welec*gshieldc(j,i) +C & +welec*gshieldc_loc(j,i) +C & +wcorr*gshieldc_ec(j,i) +C & +wcorr*gshieldc_loc_ec(j,i) +C & +wturn3*gshieldc_t3(j,i) +C & +wturn3*gshieldc_loc_t3(j,i) +C & +wturn4*gshieldc_t4(j,i) +C & ,wturn4*gshieldc_loc_t4(j,i) +C & ,wel_loc*gshieldc_ll(j,i) +C & ,wel_loc*gshieldc_loc_ll(j,i) +C & ,wtube*gg_tube(j,i) + +C print *,gg_tube(1,0),"TU3" #ifdef DEBUG write (iout,*) "gloc before adding corr" do i=1,4*nres @@ -784,7 +1010,7 @@ c#undef DEBUG call MPI_Barrier(FG_COMM,IERR) time_barrier_g=time_barrier_g+MPI_Wtime()-time00 time00=MPI_Wtime() - call MPI_Reduce(gradbufc(1,1),gradc(1,1,icg),3*nres, + call MPI_Reduce(gradbufc(1,0),gradc(1,0,icg),3*nres+3, & MPI_DOUBLE_PRECISION,MPI_SUM,king,FG_COMM,IERR) call MPI_Reduce(gradbufx(1,1),gradx(1,1,icg),3*nres, & MPI_DOUBLE_PRECISION,MPI_SUM,king,FG_COMM,IERR) @@ -933,6 +1159,7 @@ c------------------------------------------------------------------------------- include 'COMMON.IOUNITS' include 'COMMON.FFIELD' include 'COMMON.SBRIDGE' + include 'COMMON.CONTROL' double precision kfac /2.4d0/ double precision x,x2,x3,x4,x5,licznik /1.12692801104297249644/ c facT=temp0/t_bath @@ -968,6 +1195,11 @@ c facT=2*temp0/(t_bath+temp0) #endif stop 555 endif + if (shield_mode.gt.0) then + wscp=weights(2)*fact + wsc=weights(1)*fact + wvdwpp=weights(16)*fact + endif welec=weights(3)*fact wcorr=weights(4)*fact3 wcorr5=weights(5)*fact4 @@ -1022,14 +1254,16 @@ C------------------------------------------------------------------------ eliptran=energia(22) Eafmforce=energia(23) ethetacnstr=energia(24) + etube=energia(25) #ifdef SPLITELE write (iout,10) evdw,wsc,evdw2,wscp,ees,welec,evdw1,wvdwpp, & estr,wbond,ebe,wang, & escloc,wscloc,etors,wtor,etors_d,wtor_d,ehpb,wstrain, & ecorr,wcorr, & ecorr5,wcorr5,ecorr6,wcorr6,eel_loc,wel_loc,eello_turn3,wturn3, - & eello_turn4,wturn4,eello_turn6,wturn6,esccor,wsccro,edihcnstr, + & eello_turn4,wturn4,eello_turn6,wturn6,esccor,wsccor,edihcnstr, & ethetacnstr,ebr*nss,Uconst,eliptran,wliptran,Eafmforc, + & etube,wtube, & etot 10 format (/'Virtual-chain energies:'// & 'EVDW= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-SC)'/ @@ -1057,6 +1291,7 @@ C------------------------------------------------------------------------ & 'UCONST= ',1pE16.6,' (Constraint energy)'/ & 'ELT=',1pE16.6, ' WEIGHT=',1pD16.6,' (Lipid transfer energy)'/ & 'EAFM= ',1pE16.6,' (atomic-force microscopy)'/ + & 'ETUBE=',1pE16.6, ' WEIGHT=',1pD16.6,' (cylindrical energy)'/ & 'ETOT= ',1pE16.6,' (total)') #else @@ -1067,6 +1302,7 @@ C------------------------------------------------------------------------ & ecorr5,wcorr5,ecorr6,wcorr6,eel_loc,wel_loc,eello_turn3,wturn3, & eello_turn4,wturn4,eello_turn6,wturn6,esccor,wsccro,edihcnstr, & ethetacnstr,ebr*nss,Uconst,eliptran,wliptran,Eafmforc, + & etube,wtube, & etot 10 format (/'Virtual-chain energies:'// & 'EVDW= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-SC)'/ @@ -1093,6 +1329,7 @@ C------------------------------------------------------------------------ & 'UCONST=',1pE16.6,' (Constraint energy)'/ & 'ELT=',1pE16.6, ' WEIGHT=',1pD16.6,' (Lipid transfer energy)'/ & 'EAFM= ',1pE16.6,' (atomic-force microscopy)'/ + & 'ETUBE=',1pE16.6, ' WEIGHT=',1pD16.6,' (cylindrical energy)'/ & 'ETOT= ',1pE16.6,' (total)') #endif return @@ -1701,6 +1938,7 @@ C lipbufthick is thickenes of lipid buffore & +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 write(iout,*) "tu,", i,j,aa_lip(itypi,itypj),bb_lip(itypi,itypj) C if (aa.ne.aa_aq(itypi,itypj)) write(63,'(2e10.5)') C &(aa-aa_aq(itypi,itypj)),(bb-bb_aq(itypi,itypj)) C if (ssgradlipj.gt.0.0d0) print *,"??WTF??" @@ -1977,6 +2215,7 @@ C lipbufthick is thickenes of lipid buffore & +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0 C if (aa.ne.aa_aq(itypi,itypj)) write(63,'2e10.5') C &(aa-aa_aq(itypi,itypj)),(bb-bb_aq(itypi,itypj)) +C write(iout,*) "tu,", i,j,aa,bb,aa_lip(itypi,itypj),sslipi,sslipj dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2 xj_safe=xj yj_safe=yj @@ -2704,28 +2943,28 @@ c write(iout,*) 'nphi=',nphi,nres #endif #ifdef NEWCORR if (i.gt. nnt+2 .and. i.lt.nct+2) then - iti = itortyp(itype(i-2)) + 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 - iti1 = itortyp(itype(i-1)) + iti1 = itype2loc(itype(i-1)) else - iti1=ntortyp+1 + iti1=nloctyp endif c write(iout,*),i - b1(1,i-2)=bnew1(1,1,iti)*dsin(theta(i-1)/2.0) + b1(1,i-2)=bnew1(1,1,iti)*dsin(theta(i-1)/2.0d0) & +bnew1(2,1,iti)*dsin(theta(i-1)) - & +bnew1(3,1,iti)*dcos(theta(i-1)/2.0) + & +bnew1(3,1,iti)*dcos(theta(i-1)/2.0d0) gtb1(1,i-2)=bnew1(1,1,iti)*dcos(theta(i-1)/2.0d0)/2.0d0 & +bnew1(2,1,iti)*dcos(theta(i-1)) & -bnew1(3,1,iti)*dsin(theta(i-1)/2.0d0)/2.0d0 c & +bnew1(3,1,iti)*sin(alpha(i))*cos(beta(i)) c &*(cos(theta(i)/2.0) - b2(1,i-2)=bnew2(1,1,iti)*dsin(theta(i-1)/2.0) + b2(1,i-2)=bnew2(1,1,iti)*dsin(theta(i-1)/2.0d0) & +bnew2(2,1,iti)*dsin(theta(i-1)) - & +bnew2(3,1,iti)*dcos(theta(i-1)/2.0) + & +bnew2(3,1,iti)*dcos(theta(i-1)/2.0d0) c & +bnew2(3,1,iti)*sin(alpha(i))*cos(beta(i)) c &*(cos(theta(i)/2.0) gtb2(1,i-2)=bnew2(1,1,iti)*dcos(theta(i-1)/2.0d0)/2.0d0 @@ -2763,6 +3002,17 @@ c write(iout,*) 'b1=',b1(1,i-2) c write (iout,*) 'theta=', theta(i-1) enddo #else + 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 b1(1,i-2)=b(3,iti) b1(2,i-2)=b(5,iti) b2(1,i-2)=b(2,iti) @@ -2850,15 +3100,15 @@ c write (iout,*) 'theta=', theta(i-1) 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 - iti = itortyp(itype(i-2)) + iti = itype2loc(itype(i-2)) else - iti=ntortyp + 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 = itortyp(itype(i-1)) + iti1 = itype2loc(itype(i-1)) else - iti1=ntortyp + iti1=nloctyp endif cd write (iout,*) '*******i',i,' iti1',iti cd write (iout,*) 'b1',b1(:,iti) @@ -2871,8 +3121,8 @@ c if (i .gt. iatel_s+2) then 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,iti),EE(2,1,iti), -c & EE(1,2,iti),EE(2,2,iti) +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", @@ -2907,17 +3157,24 @@ c & eug(2,2,i-2) 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 + iti1=nloctyp endif else - iti1=ntortyp + iti1=nloctyp endif do k=1,2 mu(k,i-2)=Ub2(k,i-2)+b1(k,i-1) enddo -c write (iout,*) 'mu ',mu(:,i-2),i-2 +#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),eenew(1,itype2loc(iti)) +#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) @@ -3204,11 +3461,11 @@ c endif #endif #endif cd do i=1,nres -cd iti = itortyp(itype(i)) +cd iti = itype2loc(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 & (EE(j,k,i),k=1,2),(Ug(j,k,i),k=1,2),(EUg(j,k,i),k=1,2) cd enddo cd enddo return @@ -3242,6 +3499,7 @@ C 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), @@ -3326,21 +3584,23 @@ 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 - if (i.le.1) cycle +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 - & .or.((i+4).gt.nres) - & .or.((i-1).le.0) +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 & .or. itype(i+2).eq.ntyp1 & .or. itype(i+3).eq.ntyp1) cycle - if(i.gt.1)then - if(itype(i-1).eq.ntyp1)cycle - end if - if(i.LT.nres-3)then - if (itype(i+4).eq.ntyp1) cycle - end if +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) @@ -3356,23 +3616,47 @@ C end of changes by Ana if (ymedi.lt.0) ymedi=ymedi+boxysize zmedi=mod(zmedi,boxzsize) if (zmedi.lt.0) zmedi=zmedi+boxzsize + zmedi2=mod(zmedi,boxzsize) + if (zmedi2.lt.0) zmedi2=zmedi2+boxzsize + if ((zmedi2.gt.bordlipbot) + &.and.(zmedi2.lt.bordliptop)) then +C the energy transfer exist + if (zmedi2.lt.buflipbot) then +C what fraction I am in + fracinbuf=1.0d0- + & ((zmedi2-bordlipbot)/lipbufthick) +C lipbufthick is thickenes of lipid buffore + sslipi=sscalelip(fracinbuf) + ssgradlipi=-sscagradlip(fracinbuf)/lipbufthick + elseif (zmedi2.gt.bufliptop) then + fracinbuf=1.0d0-((bordliptop-zmedi2)/lipbufthick) + sslipi=sscalelip(fracinbuf) + ssgradlipi=sscagradlip(fracinbuf)/lipbufthick + else + sslipi=1.0d0 + ssgradlipi=0.0d0 + endif + else + sslipi=0.0d0 + ssgradlipi=0.0d0 + endif 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.le.1) cycle + 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 - & .or.((i+5).gt.nres) - & .or.((i-1).le.0) +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 - & .or. itype(i+5).eq.ntyp1 - & .or. itype(i).eq.ntyp1 - & .or. itype(i-1).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) @@ -3414,7 +3698,30 @@ c endif if (ymedi.lt.0) ymedi=ymedi+boxysize zmedi=mod(zmedi,boxzsize) if (zmedi.lt.0) zmedi=zmedi+boxzsize - + zmedi2=mod(zmedi,boxzsize) + if (zmedi2.lt.0) zmedi2=zmedi2+boxzsize + if ((zmedi2.gt.bordlipbot) + &.and.(zmedi2.lt.bordliptop)) then +C the energy transfer exist + if (zmedi2.lt.buflipbot) then +C what fraction I am in + fracinbuf=1.0d0- + & ((zmedi2-bordlipbot)/lipbufthick) +C lipbufthick is thickenes of lipid buffore + sslipi=sscalelip(fracinbuf) + ssgradlipi=-sscagradlip(fracinbuf)/lipbufthick + elseif (zmedi2.gt.bufliptop) then + fracinbuf=1.0d0-((bordliptop-zmedi2)/lipbufthick) + sslipi=sscalelip(fracinbuf) + ssgradlipi=sscagradlip(fracinbuf)/lipbufthick + else + sslipi=1.0d0 + ssgradlipi=0.0 + endif + else + sslipi=0.0d0 + ssgradlipi=0.0 + endif num_conti=num_cont_hb(i) c write(iout,*) "JESTEM W PETLI" call eelecij(i,i+3,ees,evdw1,eel_loc) @@ -3429,15 +3736,17 @@ 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 - if (i.le.1) cycle +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 - & .or.((i+2).gt.nres) - & .or.((i-1).le.0) +c & .or.((i+2).gt.nres) +c & .or.((i-1).le.0) C end of changes by Ana - & .or. itype(i+2).eq.ntyp1 - & .or. itype(i-1).eq.ntyp1 +c & .or. itype(i+2).eq.ntyp1 +c & .or. itype(i-1).eq.ntyp1 & ) cycle dxi=dc(1,i) dyi=dc(2,i) @@ -3454,6 +3763,29 @@ C end of changes by Ana if (ymedi.lt.0) ymedi=ymedi+boxysize zmedi=mod(zmedi,boxzsize) if (zmedi.lt.0) zmedi=zmedi+boxzsize + if ((zmedi.gt.bordlipbot) + &.and.(zmedi.lt.bordliptop)) then +C the energy transfer exist + if (zmedi.lt.buflipbot) then +C what fraction I am in + fracinbuf=1.0d0- + & ((zmedi-bordlipbot)/lipbufthick) +C lipbufthick is thickenes of lipid buffore + sslipi=sscalelip(fracinbuf) + ssgradlipi=-sscagradlip(fracinbuf)/lipbufthick + elseif (zmedi.gt.bufliptop) then + fracinbuf=1.0d0-((bordliptop-zmedi)/lipbufthick) + sslipi=sscalelip(fracinbuf) + ssgradlipi=sscagradlip(fracinbuf)/lipbufthick + else + sslipi=1.0d0 + ssgradlipi=0.0 + endif + else + sslipi=0.0d0 + ssgradlipi=0.0 + endif +C print *,sslipi,"TU?!" C xmedi=xmedi+xshift*boxxsize C ymedi=ymedi+yshift*boxysize C zmedi=zmedi+zshift*boxzsize @@ -3486,16 +3818,18 @@ 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) +C do j=16,17 C write (iout,*) i,j - if (j.le.1) cycle +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 - & .or.((j+2).gt.nres) - & .or.((j-1).le.0) +c & .or.((j+2).gt.nres) +c & .or.((j-1).le.0) C end of changes by Ana - & .or.itype(j+2).eq.ntyp1 - & .or.itype(j-1).eq.ntyp1 +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 @@ -3556,6 +3890,7 @@ 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 @@ -3585,6 +3920,28 @@ C zj=c(3,j)+0.5D0*dzj-zmedi 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" + 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 dist_init=(xj-xmedi)**2+(yj-ymedi)**2+(zj-zmedi)**2 xj_safe=xj yj_safe=yj @@ -3669,15 +4026,30 @@ c 4/26/02 - AL scaling down 1,4 repulsive VDW interactions el1=fac3*(4.0D0+fac*fac-3.0D0*(cosb*cosb+cosg*cosg)) el2=fac4*fac C MARYSIA - eesij=(el1+el2) +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 - ees=ees+eesij*fac_shield(i)*fac_shield(j) +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 +C FOR NOW SHIELD IS NOT USED WITH LIPSCALE +C & *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0) else + fac_shield(i)=1.0 + fac_shield(j)=1.0 + eesij=(el1+el2) ees=ees+eesij + &*((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0) +C print *,"TUCC",(sslipi+sslipj)/2.0d0*lipscale**2+1.0d0 endif evdw1=evdw1+evdwij*sss + & *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0) +C print *,sslipi,sslipj,lipscale**2, +C & (sslipi+sslipj)/2.0d0*lipscale**2+1.0d0 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, @@ -3687,7 +4059,9 @@ cd & xmedi,ymedi,zmedi,xj,yj,zj write (iout,'(a6,2i5,0pf7.3,2i5,2e11.3)') &'evdw1',i,j,evdwij &,iteli,itelj,aaa,evdw1 - write (iout,'(a6,2i5,0pf7.3)') 'ees',i,j,eesij + write (iout,*) sss + write (iout,'(a6,2i5,0pf7.3,2f8.3)') 'ees',i,j,eesij, + &fac_shield(i),fac_shield(j) endif C @@ -3695,27 +4069,114 @@ C Calculate contributions to the Cartesian gradient. C #ifdef SPLITELE facvdw=-6*rrmij*(ev1+evdwij)*sss + & *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0) facel=-3*rrmij*(el1+eesij) + &*((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0) fac1=fac erij(1)=xj*rmij erij(2)=yj*rmij erij(3)=zj*rmij + * * Radial derivatives. First process both termini of the fragment (i,j) * 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 + 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) +C Lipidic part for lipscale + gelc_long(3,j)=gelc_long(3,j)+ + & ssgradlipj*eesij/2.0d0*lipscale**2 + + gelc_long(3,i)=gelc_long(3,i)+ + & ssgradlipi*eesij/2.0d0*lipscale**2 + * * Loop over residues i+1 thru j-1. * @@ -3726,8 +4187,13 @@ cgrad enddo cgrad enddo if (sss.gt.0.0) then ggg(1)=facvdw*xj+sssgrad*rmij*evdwij*xj + & *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0) + ggg(2)=facvdw*yj+sssgrad*rmij*evdwij*yj + & *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0) + ggg(3)=facvdw*zj+sssgrad*rmij*evdwij*zj + & *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0) else ggg(1)=0.0 ggg(2)=0.0 @@ -3743,6 +4209,12 @@ c 9/28/08 AL Gradient compotents will be summed only at the end gvdwpp(k,j)=gvdwpp(k,j)+ggg(k) gvdwpp(k,i)=gvdwpp(k,i)-ggg(k) enddo +C Lipidic part for scaling weight + gvdwpp(3,j)=gvdwpp(3,j)+ + & sss*ssgradlipj*evdwij/2.0d0*lipscale**2 + gvdwpp(3,i)=gvdwpp(3,i)+ + & sss*ssgradlipi*evdwij/2.0d0*lipscale**2 + * * Loop over residues i+1 thru j-1. * @@ -3754,6 +4226,7 @@ cgrad enddo #else C MARYSIA facvdw=(ev1+evdwij)*sss + & *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0) facel=(el1+eesij) fac1=fac fac=-3*rrmij*(facvdw+facvdw+facel) @@ -3764,8 +4237,11 @@ C MARYSIA * Radial derivatives. First process both termini of the fragment (i,j) * 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 @@ -3786,12 +4262,22 @@ 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 + & *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0) + ggg(2)=facvdw*yj+sssgrad*rmij*evdwij*yj + & *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0) + ggg(3)=facvdw*zj+sssgrad*rmij*evdwij*zj + & *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0) do k=1,3 gvdwpp(k,j)=gvdwpp(k,j)+ggg(k) gvdwpp(k,i)=gvdwpp(k,i)-ggg(k) enddo + gvdwpp(3,j)=gvdwpp(3,j)+ + & sss*ssgradlipj*evdwij/2.0d0*lipscale**2 + gvdwpp(3,i)=gvdwpp(3,i)+ + & sss*ssgradlipi*evdwij/2.0d0*lipscale**2 + #endif * * Angular part @@ -3808,7 +4294,9 @@ c 9/28/08 AL Gradient compotents will be summed only at the end 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 + & *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0) enddo c do k=1,3 c ghalf=0.5D0*ggg(k) @@ -3824,16 +4312,23 @@ 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 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) + & +((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 + & *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0) 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) + & +((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 + & *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0) gelc_long(k,j)=gelc_long(k,j)+ggg(k) gelc_long(k,i)=gelc_long(k,i)-ggg(k) enddo +C print *,"before33", gelc_long(1,i), gelc_long(1,j) + C MARYSIA c endif !sscale IF (wel_loc.gt.0.0d0 .or. wcorr4.gt.0.0d0 .or. wcorr5.gt.0.0d0 @@ -4034,15 +4529,75 @@ cgrad endif 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) + 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) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) + +C Now derivative over eel_loc + 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=',muij(1),muij(2),muij(3),muij(4) +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) + geel_loc_ij=(a22*gmuij1(1) & +a23*gmuij1(2) & +a32*gmuij1(3) - & +a33*gmuij1(4) + & +a33*gmuij1(4)) + & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) + c write(iout,*) "derivative over thatai" c write(iout,*) a22*gmuij1(1), a23*gmuij1(2) ,a32*gmuij1(3), c & a33*gmuij1(4) @@ -4058,6 +4613,10 @@ c & a33*gmuij2(4) & +a33*gmuij2(4) gloc(nphi+i-1,icg)=gloc(nphi+i-1,icg)+ & geel_loc_ij*wel_loc + & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) + + c Derivative over j residue geel_loc_ji=a22*gmuji1(1) & +a23*gmuji1(2) @@ -4069,6 +4628,9 @@ c & a33*gmuji1(4) gloc(nphi+j,icg)=gloc(nphi+j,icg)+ & geel_loc_ji*wel_loc + & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) + geel_loc_ji= & +a22*gmuji2(1) & +a23*gmuji2(2) @@ -4079,11 +4641,14 @@ 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) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) + #endif cd write (iout,*) 'i',i,' j',j,' eel_loc_ij',eel_loc_ij - if (energy_dec) write (iout,'(a6,2i5,0pf7.3)') - & 'eelloc',i,j,eel_loc_ij + if (energy_dec) write (iout,'(a6,2i5,0pf7.3,2f7.3)') + & 'eelloc',i,j,eel_loc_ij,a22*muij(1),a23*muij(2) 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) @@ -4092,21 +4657,38 @@ c & i,j,a22,muij(1),a23,muij(2),a32,muij(3),a33,muij(4) 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) + & (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) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) + 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) + & (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) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) + 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) + 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) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) + 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 + gel_loc_long(3,j)=gel_loc_long(3,j)+ + & ssgradlipj*eel_loc_ij/2.0d0*lipscale/ + & ((sslipi+sslipj)/2.0d0*lipscale+1.0d0) + + gel_loc_long(3,i)=gel_loc_long(3,i)+ + & ssgradlipi*eel_loc_ij/2.0d0*lipscale/ + & ((sslipi+sslipj)/2.0d0*lipscale+1.0d0) + cgrad do k=i+1,j2 cgrad do l=1,3 cgrad gel_loc(l,k)=gel_loc(l,k)+ggg(l) @@ -4116,12 +4698,24 @@ 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)) + & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) + 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) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) + 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) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) + 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) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) + enddo ENDIF C Change 12/26/95 to calculate four-body contributions to H-bonding energy @@ -4200,8 +4794,18 @@ c ees0mij=dsqrt(4.0D0-cosa4+wij*wij-3.0D0*cosbg2*cosbg2) 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 @@ -4269,17 +4873,29 @@ 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) + & *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) + & *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) + & *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 C Diagnostics. Comment out or remove after debugging! cdiag do k=1,3 @@ -4331,6 +4947,7 @@ C Third- and fourth-order contributions from turns 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), @@ -4343,7 +4960,42 @@ C Third- and fourth-order contributions from turns & 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 +C xj=(c(1,j)+c(1,j+1))/2.0d0 +C yj=(c(2,j)+c(2,j+1))/2.0d0 + zj=(c(3,j)+c(3,j+1))/2.0d0 +C xj=mod(xj,boxxsize) +C if (xj.lt.0) xj=xj+boxxsize +C yj=mod(yj,boxysize) +C 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" + 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 +C sslipj=0.0 +C ssgradlipj=0.0d0 + +C write (iout,*) "eturn3",i,j,j1,j2 a_temp(1,1)=a22 a_temp(1,2)=a23 a_temp(2,1)=a32 @@ -4371,15 +5023,82 @@ c auxalary matrix for i+2 and constant i+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)) - eello_turn3=eello_turn3+0.5d0*(pizda(1,1)+pizda(2,2)) + if (shield_mode.eq.0) then + fac_shield(i)=1.0d0 + fac_shield(j)=1.0d0 +C else +C fac_shield(i)=0.4 +C fac_shield(j)=0.6 + endif +C if (j.eq.78) +C & write(iout,*) i,j,fac_shield(i),fac_shield(j) + eello_turn3=eello_turn3+ +C & 1.0*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) + &0.5d0*(pizda(1,1)+pizda(2,2)) + & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) + eello_t3= + &0.5d0*(pizda(1,1)+pizda(2,2)) + & *fac_shield(i)*fac_shield(j) +#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) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) + 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) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) - if (energy_dec) write (iout,'(a6,2i5,0pf7.3)') - & 'eturn3',i,j,0.5d0*(pizda(1,1)+pizda(2,2)) +#endif + +C if (energy_dec) write (iout,'(a6,2i5,0pf7.3)') +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 @@ -4388,12 +5107,18 @@ C Derivatives in gamma(i) 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) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) + 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),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) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) + C Cartesian derivatives do l=1,3 c ghalf1=0.5d0*agg(l,1) @@ -4407,6 +5132,9 @@ c ghalf4=0.5d0*agg(l,4) 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)) + & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) + 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) @@ -4414,6 +5142,8 @@ c ghalf4=0.5d0*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)) + & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) a_temp(1,1)=aggj(l,1)!+ghalf1 a_temp(1,2)=aggj(l,2)!+ghalf2 a_temp(2,1)=aggj(l,3)!+ghalf3 @@ -4421,6 +5151,9 @@ c ghalf4=0.5d0*agg(l,4) 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) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) + a_temp(1,1)=aggj1(l,1) a_temp(1,2)=aggj1(l,2) a_temp(2,1)=aggj1(l,3) @@ -4428,7 +5161,19 @@ c ghalf4=0.5d0*agg(l,4) 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) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) enddo + gshieldc_t3(3,i)=gshieldc_t3(3,i)+ + & ssgradlipi*eello_t3/4.0d0*lipscale + gshieldc_t3(3,j)=gshieldc_t3(3,j)+ + & ssgradlipj*eello_t3/4.0d0*lipscale + gshieldc_t3(3,i-1)=gshieldc_t3(3,i-1)+ + & ssgradlipi*eello_t3/4.0d0*lipscale + gshieldc_t3(3,j-1)=gshieldc_t3(3,j-1)+ + & ssgradlipj*eello_t3/4.0d0*lipscale + +C print *,ssgradlipi,ssgradlipj,eello_t3,sslipi,sslipj return end C------------------------------------------------------------------------------- @@ -4448,6 +5193,7 @@ C Third- and fourth-order contributions from turns 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), @@ -4476,13 +5222,44 @@ CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC cd call checkint_turn4(i,a_temp,eello_turn4_num) c write (iout,*) "eturn4 i",i," j",j," j1",j1," j2",j2 c write(iout,*)"WCHODZE W PROGRAM" + zj=(c(3,j)+c(3,j+1))/2.0d0 +C xj=mod(xj,boxxsize) +C if (xj.lt.0) xj=xj+boxxsize +C yj=mod(yj,boxysize) +C if (yj.lt.0) yj=yj+boxysize + zj=mod(zj,boxzsize) + if (zj.lt.0) zj=zj+boxzsize +C if ((zj.lt.0).or.(xj.lt.0).or.(yj.lt.0)) write (*,*) "CHUJ" + 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 + a_temp(1,1)=a22 a_temp(1,2)=a23 a_temp(2,1)=a32 a_temp(2,2)=a33 - iti1=itortyp(itype(i+1)) - iti2=itortyp(itype(i+2)) - iti3=itortyp(itype(i+3)) + 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)) @@ -4548,20 +5325,88 @@ c i+3 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) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) + + 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 -cd write (2,*) 'i,',i,' j',j,'eello_turn4',-(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) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) + gloc(nphi+i+1,icg)= gloc(nphi+i+1,icg) & -(gs23+gs21+gsEE2)*wturn4 + & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) + gloc(nphi+i+2,icg)= gloc(nphi+i+2,icg) & -(gs32+gsE31+gsEE3)*wturn4 + & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) + c gloc(nphi+i+1,icg)=gloc(nphi+i+1,icg)- c & gs2 #endif @@ -4577,6 +5422,9 @@ C Derivatives in gamma(i) 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) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) + 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)) @@ -4585,6 +5433,9 @@ C Derivatives in gamma(i+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) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) + 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)) @@ -4596,6 +5447,9 @@ C Derivatives in gamma(i+2) 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) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) + C Cartesian derivatives C Derivatives of this turn contributions in DC(i+2) if (j.lt.nres-1) then @@ -4615,6 +5469,9 @@ C Derivatives of this turn contributions in DC(i+2) 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) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) + enddo endif C Remaining derivatives of this turn contribution @@ -4633,6 +5490,9 @@ C Remaining derivatives of this turn contribution 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) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) + a_temp(1,1)=aggi1(l,1) a_temp(1,2)=aggi1(l,2) a_temp(2,1)=aggi1(l,3) @@ -4647,6 +5507,9 @@ C Remaining derivatives of this turn contribution 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) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) + a_temp(1,1)=aggj(l,1) a_temp(1,2)=aggj(l,2) a_temp(2,1)=aggj(l,3) @@ -4661,6 +5524,9 @@ C Remaining derivatives of this turn contribution 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) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) + a_temp(1,1)=aggj1(l,1) a_temp(1,2)=aggj1(l,2) a_temp(2,1)=aggj1(l,3) @@ -4676,7 +5542,17 @@ C Remaining derivatives of this turn contribution 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) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) enddo + gshieldc_t4(3,i)=gshieldc_t4(3,i)+ + & ssgradlipi*eello_t4/4.0d0*lipscale + gshieldc_t4(3,j)=gshieldc_t4(3,j)+ + & ssgradlipj*eello_t4/4.0d0*lipscale + gshieldc_t4(3,i-1)=gshieldc_t4(3,i-1)+ + & ssgradlipi*eello_t4/4.0d0*lipscale + gshieldc_t4(3,j-1)=gshieldc_t4(3,j-1)+ + & ssgradlipj*eello_t4/4.0d0*lipscale return end C----------------------------------------------------------------------------- @@ -5418,6 +6294,7 @@ C Checking if it involves dummy (NH3+ or COO-) group if (itype(i-1).eq.ntyp1 .or. itype(i).eq.ntyp1) then C YES vbldpDUM is the equlibrium length of spring for Dummy atom diff = vbld(i)-vbldpDUM + if (energy_dec) write(iout,*) "dum_bond",i,diff else C NO vbldp0 is the equlibrium lenght of spring for peptide group diff = vbld(i)-vbldp0 @@ -5431,6 +6308,7 @@ C NO vbldp0 is the equlibrium lenght of spring for peptide group c write (iout,'(i5,3f10.5)') i,(gradb(j,i-1),j=1,3) c endif enddo + estr=0.5d0*AKP*estr+estr1 c c 09/18/07 AL: multimodal bond potential based on AM1 CA-SC PMF's included @@ -5451,6 +6329,9 @@ c else do j=1,nbi diff=vbld(i+nres)-vbldsc0(j,iti) + if (energy_dec) write (iout,*) + & "estr sc",i,iti,vbld(i+nres),vbldsc0(j,iti),diff, + & AKSC(j,iti),AKSC(j,iti)*diff*diff ud(j)=aksc(j,iti)*diff u(j)=abond0(j,iti)+0.5d0*ud(j)*diff enddo @@ -5784,6 +6665,7 @@ C etheta=0.0D0 do i=ithet_start,ithet_end c print *,i,itype(i-1),itype(i),itype(i-2) +C if (itype(i-1).eq.ntyp1) cycle if ((itype(i-1).eq.ntyp1).or.itype(i-2).eq.ntyp1 & .or.itype(i).eq.ntyp1) cycle C print *,i,theta(i) @@ -7033,6 +7915,252 @@ C v1cij=v1c(1,j,itori,itori1,itori2,iblock,ntblock) return end #endif +C---------------------------------------------------------------------------------- +C The rigorous attempt to derive energy function + subroutine etor_kcc(etors,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' + logical lprn +c double precision thybt1(maxtermkcc),thybt2(maxtermkcc) +C Set lprn=.true. for debugging + lprn=.false. +c lprn=.true. +C print *,"wchodze kcc" + if (lprn) write (iout,*) "etor_kcc tor_mode",tor_mode + if (tor_mode.ne.2) then + etors=0.0D0 + endif + 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_kcc(itype(i-2)) + itori1=itortyp_kcc(itype(i-1)) + phii=phi(i) + glocig=0.0D0 + glocit1=0.0d0 + glocit2=0.0d0 + sumnonchebyshev=0.0d0 + sumchebyshev=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 Cosines of halves thetas + costheti12=0.5d0*(1.0d0+costhet1) + costheti22=0.5d0*(1.0d0+costhet2) +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 + etori=0.0d0 + do j=1,nterm_kcc(itori,itori1) + + nval=nterm_kcc_Tb(itori,itori1) + v1ij=v1_kcc(j,itori,itori1) + v2ij=v2_kcc(j,itori,itori1) +c write (iout,*) "i",i," j",j," v1",v1ij," v2",v2ij +C v1ij is c_n and d_n in euation above + cosphi=dcos(j*phii) + sinphi=dsin(j*phii) + sint1t2n1=sint1t2n + sint1t2n=sint1t2n*sint1t2 + sumth1tyb1=tschebyshev(1,nval,v11_chyb(1,j,itori,itori1), + & costheti12) + gradth1tyb1=-0.5d0*sinthet1*gradtschebyshev(0,nval-1, + & v11_chyb(1,j,itori,itori1),costheti12) +c write (iout,*) "v11",(v11_chyb(k,j,itori,itori1),k=1,nval), +c & " sumth1tyb1",sumth1tyb1," gradth1tyb1",gradth1tyb1 + sumth2tyb1=tschebyshev(1,nval,v21_chyb(1,j,itori,itori1), + & costheti22) + gradth2tyb1=-0.5d0*sinthet2*gradtschebyshev(0,nval-1, + & v21_chyb(1,j,itori,itori1),costheti22) +c write (iout,*) "v21",(v21_chyb(k,j,itori,itori1),k=1,nval), +c & " sumth2tyb1",sumth2tyb1," gradth2tyb1",gradth2tyb1 + sumth1tyb2=tschebyshev(1,nval,v12_chyb(1,j,itori,itori1), + & costheti12) + gradth1tyb2=-0.5d0*sinthet1*gradtschebyshev(0,nval-1, + & v12_chyb(1,j,itori,itori1),costheti12) +c write (iout,*) "v12",(v12_chyb(k,j,itori,itori1),k=1,nval), +c & " sumth1tyb2",sumth1tyb2," gradth1tyb2",gradth1tyb2 + sumth2tyb2=tschebyshev(1,nval,v22_chyb(1,j,itori,itori1), + & costheti22) + gradth2tyb2=-0.5d0*sinthet2*gradtschebyshev(0,nval-1, + & v22_chyb(1,j,itori,itori1),costheti22) +c write (iout,*) "v22",(v22_chyb(k,j,itori,itori1),k=1,nval), +c & " sumth2tyb2",sumth2tyb2," gradth2tyb2",gradth2tyb2 +C etors=etors+sint1t2n*(v1ij*cosphi+v2ij*sinphi) +C if (energy_dec) etors_ii=etors_ii+ +C & v1ij*cosphi+v2ij*sinphi +C glocig is the gradient local i site in gamma + actval1=v1ij*cosphi*(1.0d0+sumth1tyb1+sumth2tyb1) + actval2=v2ij*sinphi*(1.0d0+sumth1tyb2+sumth2tyb2) + etori=etori+sint1t2n*(actval1+actval2) + glocig=glocig+ + & j*sint1t2n*(v2ij*cosphi*(1.0d0+sumth1tyb2+sumth2tyb2) + & -v1ij*sinphi*(1.0d0+sumth1tyb1+sumth2tyb1)) +C now gradient over theta_1 + glocit1=glocit1+ + & j*sint1t2n1*costhet1*sinthet2*(actval1+actval2)+ + & sint1t2n*(v1ij*cosphi*gradth1tyb1+v2ij*sinphi*gradth1tyb2) + glocit2=glocit2+ + & j*sint1t2n1*sinthet1*costhet2*(actval1+actval2)+ + & sint1t2n*(v1ij*cosphi*gradth2tyb1+v2ij*sinphi*gradth2tyb2) + +C now the Czebyshev polinominal sum +c do k=1,nterm_kcc_Tb(itori,itori1) +c thybt1(k)=v1_chyb(k,j,itori,itori1) +c thybt2(k)=v2_chyb(k,j,itori,itori1) +C thybt1(k)=0.0 +C thybt2(k)=0.0 +c enddo +C print *, sumth1thyb, gradthybt1, sumth2thyb, gradthybt2, +C & gradtschebyshev +C & (0,nterm_kcc_Tb(itori,itori1)-1,thybt2(1), +C & dcos(theti22)**2), +C & dsin(theti22) + +C now overal sumation +C print *,"sumnon", sumnonchebyshev,sumth1thyb+sumth2thyb + 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 +C gloc(i-3,icg)=gloc(i-3,icg)+wtor*gloci +! 6/20/98 - dihedral angle constraints + if (tor_mode.ne.2) then + edihcnstr=0.0d0 +c do i=1,ndih_constr + 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 The rigorous attempt to derive energy function + subroutine ebend_kcc(etheta,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' + logical lprn + double precision thybt1(maxtermkcc) +C Set lprn=.true. for debugging + lprn=.false. +c lprn=.true. +C print *,"wchodze kcc" + if (lprn) write (iout,*) "ebend_kcc tor_mode",tor_mode + if (tor_mode.ne.2) 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=itortyp_kcc(itype(i-1)) + sinthet=dsin(theta(i)/2.0d0) + costhet=dcos(theta(i)/2.0d0) + do j=1,nbend_kcc_Tb(iti) + thybt1(j)=v1bend_chyb(j,iti) + enddo + sumth1thyb=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*(-0.5d0) + enddo + if (tor_mode.ne.2) then + 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 + endif + return + end c------------------------------------------------------------------------------ subroutine eback_sc_corr(esccor) c 7/21/2007 Correlations between the backbone-local and side-chain-local @@ -7095,6 +8223,9 @@ c 3 = SC...Ca...Ca...SCi esccor=esccor+v1ij*cosphi+v2ij*sinphi gloci=gloci+j*(v2ij*cosphi-v1ij*sinphi) enddo + if (energy_dec) write(iout,'(a9,2i4,f8.3,3i4)') "esccor",i,j, + & esccor,intertyp, + & isccori, isccori1 c write (iout,*) "EBACK_SC_COR",i,v1ij*cosphi+v2ij*sinphi,intertyp gloc_sc(intertyp,i-3,icg)=gloc_sc(intertyp,i-3,icg)+wsccor*gloci if (lprn) @@ -7174,6 +8305,7 @@ c------------------------------------------------------------------------------ include 'COMMON.DERIV' include 'COMMON.INTERACT' include 'COMMON.CONTACTS' + include 'COMMON.SHIELD' double precision gx(3),gx1(3) logical lprn lprn=.false. @@ -7592,6 +8724,7 @@ C This subroutine calculates multi-body contributions to hydrogen-bonding include 'COMMON.CONTACTS' include 'COMMON.CHAIN' include 'COMMON.CONTROL' + include 'COMMON.SHIELD' double precision gx(3),gx1(3) integer num_cont_hb_old(maxres) logical lprn,ldone @@ -7894,6 +9027,7 @@ 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,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) @@ -8013,9 +9147,12 @@ 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) @@ -8024,6 +9161,8 @@ 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 @@ -8036,7 +9175,7 @@ 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. -c ecorr=ecorr+ekont*ees +C ecorr=ecorr+ekont*ees C Calculate multi-body contributions to the gradient. coeffpees0pij=coeffp*ees0pij coeffmees0mij=coeffm*ees0mij @@ -8087,7 +9226,89 @@ 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 @@ -8108,9 +9329,9 @@ 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 + itj1=nloctyp endif do iii=1,2 dipi(iii,1)=Ub2(iii,i) @@ -8198,16 +9419,16 @@ cd write (iout,*) "a_chujkl",((a_chuj(iii,jjj,kk,k),iii=1,2),jjj=1,2) 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 + 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 + itl1=nloctyp endif C A1 kernel(j+1) A2T cd do iii=1,2 @@ -8351,17 +9572,17 @@ 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 + 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 + 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), @@ -8699,9 +9920,9 @@ 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 @@ -8770,7 +9991,7 @@ C Cartesian gradient c goto 1112 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) @@ -8851,7 +10072,7 @@ C Cartesian gradient cd goto 1112 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) @@ -8924,7 +10145,7 @@ C Cartesian gradient cd goto 1112 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) @@ -9221,7 +10442,7 @@ 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)) @@ -9513,16 +10734,16 @@ 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 + 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 + itl1=nloctyp endif #ifdef MOMENT s1=dip(4,jj,i)*dip(4,kk,k) @@ -9531,7 +10752,7 @@ C energy moment and not to the cluster cumulant. 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,itk),auxmat(1,1)) + 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) @@ -9629,24 +10850,24 @@ 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 + 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 + 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 + 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, @@ -9866,11 +11087,11 @@ c 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 @@ -10354,7 +11575,7 @@ 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 + if (positi.le.0.0) 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 @@ -10530,11 +11751,12 @@ C first for shielding is setting of function of side-chains 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/ + &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) + &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 @@ -10543,14 +11765,17 @@ 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(k+nres,j)-(c(i,j)+c(i+1,j))/2.0d0 + 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(k+nres,j)-c(k,j) - pept_group(j)=c(i,j)-c(i+1,j) + 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 @@ -10558,8 +11783,14 @@ C lets have their lenght 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 @@ -10567,7 +11798,7 @@ 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))=k + 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 @@ -10577,20 +11808,29 @@ C Lets have the sscale value else scale_fac_dist=-sh_frac_dist*sh_frac_dist & *(2.0*sh_frac_dist-3.0d0) - fac_help_scale=6.0*(scale_fac_dist-scale_fac_dist**2) + 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+short**2/dist_pep_side**2) + costhet=1.0d0/dsqrt(1.0+short**2/dist_pep_side**2) C now costhet_grad - costhet_fac=costhet**3*short**2*(-0.5)/dist_pep_side**3 +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 @@ -10602,40 +11842,981 @@ C pep_side0pept_group is vector multiplication do j=1,3 pep_side0pept_group=pep_side0pept_group+pep_side(j)*side_calf(j) enddo - fac_alfa_sin=1.0-(pep_side0pept_group/ - & (dist_pep_side*dist_side_calf))**2 + 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 - cosphi=1.0d0/dsqrt(1+rkprim**2/dist_pep_side**2) +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)*VofOverlap + & +(sh_frac_dist_grad(j) C gradient po costhet - &+scale_fac_dist*costhet_grad(j) + &-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)*VofOverlap*2.0d0 - & +scale_fac_dist*costhet_grad(j)*2.0d0 -C grad_shield_side_ca is Calfa sidechain gradient - grad_shield_side_ca(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 -C if ((cosphi.le.0.0).or.(costhet.le.0.0)) write(iout,*) "ERROR", -C & cosphi,costhet -C now should be fac_side_grad(k) which will be gradient of factor k which also -C affect the gradient of peptide group i fac_pept_grad(i) and i+1 - write(2,*) "myvolume",VofOverlap,VSolvSphere_div,VolumeTotal - enddo -C write(2,*) "TOTAL VOLUME",i,VolumeTotal -C the scaling factor of the shielding effect + enddo fac_shield(i)=VolumeTotal*div77_81+div4_81 - write(2,*) "TOTAL VOLUME",i,VolumeTotal,fac_shield(i) +C write(2,*) "TOTAL VOLUME",i,VolumeTotal,fac_shield(i) 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 +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' + include 'COMMON.LOCAL' + +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 write(2,*) "ivec",ivec_start,ivec_end + do i=1,nres + fac_shield(i)=0.0d0 + do j=1,3 + grad_shield(j,i)=0.0d0 + enddo + enddo +C the line belowe needs to be changed for FGPROC>1 + do i=ivec_start,ivec_end +C do i=1,nres-1 +C if ((itype(i).eq.ntyp1).and.itype(i+1).eq.ntyp1) cycle + ishield_list(i)=0 + if ((itype(i).eq.ntyp1).and.itype(i+1).eq.ntyp1) cycle +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 print *,ishield_list(i),i +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,itype(i),fac_shield(i) + enddo + return + end +C----------------------------------------------------------------------- +C----------------------------------------------------------- +C This subroutine is to mimic the histone like structure but as well can be +C utilizet to nanostructures (infinit) small modification has to be used to +C make it finite (z gradient at the ends has to be changes as well as the x,y +C gradient has to be modified at the ends +C The energy function is Kihara potential +C E=4esp*((sigma/(r-r0))^12 - (sigma/(r-r0))^6) +C 4eps is depth of well sigma is r_minimum r is distance from center of tube +C and r0 is the excluded size of nanotube (can be set to 0 if we want just a +C simple Kihara potential + subroutine calctube(Etube) + 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.NAMES' + include 'COMMON.INTERACT' + include 'COMMON.IOUNITS' + include 'COMMON.CALC' + include 'COMMON.CONTROL' + include 'COMMON.SPLITELE' + include 'COMMON.SBRIDGE' + double precision tub_r,vectube(3),enetube(maxres*2) + Etube=0.0d0 + do i=itube_start,itube_end + enetube(i)=0.0d0 + enetube(i+nres)=0.0d0 + enddo +C first we calculate the distance from tube center +C first sugare-phosphate group for NARES this would be peptide group +C for UNRES + do i=itube_start,itube_end +C lets ommit dummy atoms for now + if ((itype(i).eq.ntyp1).or.(itype(i+1).eq.ntyp1)) cycle +C now calculate distance from center of tube and direction vectors + xmin=boxxsize + ymin=boxysize + do j=-1,1 + vectube(1)=mod((c(1,i)+c(1,i+1))/2.0d0,boxxsize) + vectube(1)=vectube(1)+boxxsize*j + vectube(2)=mod((c(2,i)+c(2,i+1))/2.0d0,boxysize) + vectube(2)=vectube(2)+boxysize*j + + xminact=abs(vectube(1)-tubecenter(1)) + yminact=abs(vectube(2)-tubecenter(2)) + if (xmin.gt.xminact) then + xmin=xminact + xtemp=vectube(1) + endif + if (ymin.gt.yminact) then + ymin=yminact + ytemp=vectube(2) + endif + enddo + vectube(1)=xtemp + vectube(2)=ytemp + vectube(1)=vectube(1)-tubecenter(1) + vectube(2)=vectube(2)-tubecenter(2) + +C print *,"x",(c(1,i)+c(1,i+1))/2.0d0,tubecenter(1) +C print *,"y",(c(2,i)+c(2,i+1))/2.0d0,tubecenter(2) + +C as the tube is infinity we do not calculate the Z-vector use of Z +C as chosen axis + vectube(3)=0.0d0 +C now calculte the distance + tub_r=dsqrt(vectube(1)**2+vectube(2)**2+vectube(3)**2) +C now normalize vector + vectube(1)=vectube(1)/tub_r + vectube(2)=vectube(2)/tub_r +C calculte rdiffrence between r and r0 + rdiff=tub_r-tubeR0 +C and its 6 power + rdiff6=rdiff**6.0d0 +C for vectorization reasons we will sumup at the end to avoid depenence of previous + enetube(i)=pep_aa_tube/rdiff6**2.0d0+pep_bb_tube/rdiff6 +C write(iout,*) "TU13",i,rdiff6,enetube(i) +C print *,rdiff,rdiff6,pep_aa_tube +C pep_aa_tube and pep_bb_tube are precomputed values A=4eps*sigma^12 B=4eps*sigma^6 +C now we calculate gradient + fac=(-12.0d0*pep_aa_tube/rdiff6- + & 6.0d0*pep_bb_tube)/rdiff6/rdiff +C write(iout,'(a5,i4,f12.1,3f12.5)') "TU13",i,rdiff6,enetube(i), +C &rdiff,fac + +C now direction of gg_tube vector + do j=1,3 + gg_tube(j,i-1)=gg_tube(j,i-1)+vectube(j)*fac/2.0d0 + gg_tube(j,i)=gg_tube(j,i)+vectube(j)*fac/2.0d0 + enddo + enddo +C basically thats all code now we split for side-chains (REMEMBER to sum up at the END) +C print *,gg_tube(1,0),"TU" + + + do i=itube_start,itube_end +C Lets not jump over memory as we use many times iti + iti=itype(i) +C lets ommit dummy atoms for now + if ((iti.eq.ntyp1) +C in UNRES uncomment the line below as GLY has no side-chain... +C .or.(iti.eq.10) + & ) cycle + xmin=boxxsize + ymin=boxysize + do j=-1,1 + vectube(1)=mod((c(1,i+nres)),boxxsize) + vectube(1)=vectube(1)+boxxsize*j + vectube(2)=mod((c(2,i+nres)),boxysize) + vectube(2)=vectube(2)+boxysize*j + + xminact=abs(vectube(1)-tubecenter(1)) + yminact=abs(vectube(2)-tubecenter(2)) + if (xmin.gt.xminact) then + xmin=xminact + xtemp=vectube(1) + endif + if (ymin.gt.yminact) then + ymin=yminact + ytemp=vectube(2) + endif + enddo + vectube(1)=xtemp + vectube(2)=ytemp +C write(iout,*), "tututu", vectube(1),tubecenter(1),vectube(2), +C & tubecenter(2) + vectube(1)=vectube(1)-tubecenter(1) + vectube(2)=vectube(2)-tubecenter(2) + +C as the tube is infinity we do not calculate the Z-vector use of Z +C as chosen axis + vectube(3)=0.0d0 +C now calculte the distance + tub_r=dsqrt(vectube(1)**2+vectube(2)**2+vectube(3)**2) +C now normalize vector + vectube(1)=vectube(1)/tub_r + vectube(2)=vectube(2)/tub_r + +C calculte rdiffrence between r and r0 + rdiff=tub_r-tubeR0 +C and its 6 power + rdiff6=rdiff**6.0d0 +C for vectorization reasons we will sumup at the end to avoid depenence of previous + sc_aa_tube=sc_aa_tube_par(iti) + sc_bb_tube=sc_bb_tube_par(iti) + enetube(i+nres)=sc_aa_tube/rdiff6**2.0d0+sc_bb_tube/rdiff6 +C pep_aa_tube and pep_bb_tube are precomputed values A=4eps*sigma^12 B=4eps*sigma^6 +C now we calculate gradient + fac=-12.0d0*sc_aa_tube/rdiff6**2.0d0/rdiff- + & 6.0d0*sc_bb_tube/rdiff6/rdiff +C now direction of gg_tube vector + do j=1,3 + gg_tube_SC(j,i)=gg_tube_SC(j,i)+vectube(j)*fac + gg_tube(j,i-1)=gg_tube(j,i-1)+vectube(j)*fac + enddo + enddo + do i=itube_start,itube_end + Etube=Etube+enetube(i)+enetube(i+nres) + enddo +C print *,"ETUBE", etube + return + end +C TO DO 1) add to total energy +C 2) add to gradient summation +C 3) add reading parameters (AND of course oppening of PARAM file) +C 4) add reading the center of tube +C 5) add COMMONs +C 6) add to zerograd + +C----------------------------------------------------------------------- +C----------------------------------------------------------- +C This subroutine is to mimic the histone like structure but as well can be +C utilizet to nanostructures (infinit) small modification has to be used to +C make it finite (z gradient at the ends has to be changes as well as the x,y +C gradient has to be modified at the ends +C The energy function is Kihara potential +C E=4esp*((sigma/(r-r0))^12 - (sigma/(r-r0))^6) +C 4eps is depth of well sigma is r_minimum r is distance from center of tube +C and r0 is the excluded size of nanotube (can be set to 0 if we want just a +C simple Kihara potential + subroutine calctube2(Etube) + 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.NAMES' + include 'COMMON.INTERACT' + include 'COMMON.IOUNITS' + include 'COMMON.CALC' + include 'COMMON.CONTROL' + include 'COMMON.SPLITELE' + include 'COMMON.SBRIDGE' + double precision tub_r,vectube(3),enetube(maxres*2) + Etube=0.0d0 + do i=itube_start,itube_end + enetube(i)=0.0d0 + enetube(i+nres)=0.0d0 + enddo +C first we calculate the distance from tube center +C first sugare-phosphate group for NARES this would be peptide group +C for UNRES + do i=itube_start,itube_end +C lets ommit dummy atoms for now + + if ((itype(i).eq.ntyp1).or.(itype(i+1).eq.ntyp1)) cycle +C now calculate distance from center of tube and direction vectors +C vectube(1)=mod((c(1,i)+c(1,i+1))/2.0d0,boxxsize) +C if (vectube(1).lt.0) vectube(1)=vectube(1)+boxxsize +C vectube(2)=mod((c(2,i)+c(2,i+1))/2.0d0,boxysize) +C if (vectube(2).lt.0) vectube(2)=vectube(2)+boxysize + xmin=boxxsize + ymin=boxysize + do j=-1,1 + vectube(1)=mod((c(1,i)+c(1,i+1))/2.0d0,boxxsize) + vectube(1)=vectube(1)+boxxsize*j + vectube(2)=mod((c(2,i)+c(2,i+1))/2.0d0,boxysize) + vectube(2)=vectube(2)+boxysize*j + + xminact=abs(vectube(1)-tubecenter(1)) + yminact=abs(vectube(2)-tubecenter(2)) + if (xmin.gt.xminact) then + xmin=xminact + xtemp=vectube(1) + endif + if (ymin.gt.yminact) then + ymin=yminact + ytemp=vectube(2) + endif + enddo + vectube(1)=xtemp + vectube(2)=ytemp + vectube(1)=vectube(1)-tubecenter(1) + vectube(2)=vectube(2)-tubecenter(2) + +C print *,"x",(c(1,i)+c(1,i+1))/2.0d0,tubecenter(1) +C print *,"y",(c(2,i)+c(2,i+1))/2.0d0,tubecenter(2) + +C as the tube is infinity we do not calculate the Z-vector use of Z +C as chosen axis + vectube(3)=0.0d0 +C now calculte the distance + tub_r=dsqrt(vectube(1)**2+vectube(2)**2+vectube(3)**2) +C now normalize vector + vectube(1)=vectube(1)/tub_r + vectube(2)=vectube(2)/tub_r +C calculte rdiffrence between r and r0 + rdiff=tub_r-tubeR0 +C and its 6 power + rdiff6=rdiff**6.0d0 +C THIS FRAGMENT MAKES TUBE FINITE + positi=mod((c(3,i)+c(3,i+1))/2.0d0,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) + print *,positi,bordtubebot,buftubebot,bordtubetop + if ((positi.gt.bordtubebot) + & .and.(positi.lt.bordtubetop)) then +C the energy transfer exist + if (positi.lt.buftubebot) then + fracinbuf=1.0d0- + & ((positi-bordtubebot)/tubebufthick) +C lipbufthick is thickenes of lipid buffore + sstube=sscalelip(fracinbuf) + ssgradtube=-sscagradlip(fracinbuf)/tubebufthick + print *,ssgradtube, sstube,tubetranene(itype(i)) + enetube(i)=enetube(i)+sstube*tubetranenepep +C gg_tube_SC(3,i)=gg_tube_SC(3,i) +C &+ssgradtube*tubetranene(itype(i)) +C gg_tube(3,i-1)= gg_tube(3,i-1) +C &+ssgradtube*tubetranene(itype(i)) +C print *,"doing sccale for lower part" + elseif (positi.gt.buftubetop) then + fracinbuf=1.0d0- + &((bordtubetop-positi)/tubebufthick) + sstube=sscalelip(fracinbuf) + ssgradtube=sscagradlip(fracinbuf)/tubebufthick + enetube(i)=enetube(i)+sstube*tubetranenepep +C gg_tube_SC(3,i)=gg_tube_SC(3,i) +C &+ssgradtube*tubetranene(itype(i)) +C gg_tube(3,i-1)= gg_tube(3,i-1) +C &+ssgradtube*tubetranene(itype(i)) +C print *, "doing sscalefor top part",sslip,fracinbuf + else + sstube=1.0d0 + ssgradtube=0.0d0 + enetube(i)=enetube(i)+sstube*tubetranenepep +C print *,"I am in true lipid" + endif + else +C sstube=0.0d0 +C ssgradtube=0.0d0 + cycle + endif ! if in lipid or buffor + +C for vectorization reasons we will sumup at the end to avoid depenence of previous + enetube(i)=enetube(i)+sstube* + &(pep_aa_tube/rdiff6**2.0d0+pep_bb_tube/rdiff6) +C write(iout,*) "TU13",i,rdiff6,enetube(i) +C print *,rdiff,rdiff6,pep_aa_tube +C pep_aa_tube and pep_bb_tube are precomputed values A=4eps*sigma^12 B=4eps*sigma^6 +C now we calculate gradient + fac=(-12.0d0*pep_aa_tube/rdiff6- + & 6.0d0*pep_bb_tube)/rdiff6/rdiff*sstube +C write(iout,'(a5,i4,f12.1,3f12.5)') "TU13",i,rdiff6,enetube(i), +C &rdiff,fac + +C now direction of gg_tube vector + do j=1,3 + gg_tube(j,i-1)=gg_tube(j,i-1)+vectube(j)*fac/2.0d0 + gg_tube(j,i)=gg_tube(j,i)+vectube(j)*fac/2.0d0 + enddo + gg_tube(3,i)=gg_tube(3,i) + &+ssgradtube*enetube(i)/sstube/2.0d0 + gg_tube(3,i-1)= gg_tube(3,i-1) + &+ssgradtube*enetube(i)/sstube/2.0d0 + + enddo +C basically thats all code now we split for side-chains (REMEMBER to sum up at the END) +C print *,gg_tube(1,0),"TU" + do i=itube_start,itube_end +C Lets not jump over memory as we use many times iti + iti=itype(i) +C lets ommit dummy atoms for now + if ((iti.eq.ntyp1) +C in UNRES uncomment the line below as GLY has no side-chain... + & .or.(iti.eq.10) + & ) cycle + vectube(1)=c(1,i+nres) + vectube(1)=mod(vectube(1),boxxsize) + if (vectube(1).lt.0) vectube(1)=vectube(1)+boxxsize + vectube(2)=c(2,i+nres) + vectube(2)=mod(vectube(2),boxysize) + if (vectube(2).lt.0) vectube(2)=vectube(2)+boxysize + + vectube(1)=vectube(1)-tubecenter(1) + vectube(2)=vectube(2)-tubecenter(2) +C THIS FRAGMENT MAKES TUBE FINITE + 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) + print *,positi,bordtubebot,buftubebot,bordtubetop + if ((positi.gt.bordtubebot) + & .and.(positi.lt.bordtubetop)) then +C the energy transfer exist + if (positi.lt.buftubebot) then + fracinbuf=1.0d0- + & ((positi-bordtubebot)/tubebufthick) +C lipbufthick is thickenes of lipid buffore + sstube=sscalelip(fracinbuf) + ssgradtube=-sscagradlip(fracinbuf)/tubebufthick + print *,ssgradtube, sstube,tubetranene(itype(i)) + enetube(i+nres)=enetube(i+nres)+sstube*tubetranene(itype(i)) +C gg_tube_SC(3,i)=gg_tube_SC(3,i) +C &+ssgradtube*tubetranene(itype(i)) +C gg_tube(3,i-1)= gg_tube(3,i-1) +C &+ssgradtube*tubetranene(itype(i)) +C print *,"doing sccale for lower part" + elseif (positi.gt.buftubetop) then + fracinbuf=1.0d0- + &((bordtubetop-positi)/tubebufthick) + sstube=sscalelip(fracinbuf) + ssgradtube=sscagradlip(fracinbuf)/tubebufthick + enetube(i+nres)=enetube(i+nres)+sstube*tubetranene(itype(i)) +C gg_tube_SC(3,i)=gg_tube_SC(3,i) +C &+ssgradtube*tubetranene(itype(i)) +C gg_tube(3,i-1)= gg_tube(3,i-1) +C &+ssgradtube*tubetranene(itype(i)) +C print *, "doing sscalefor top part",sslip,fracinbuf + else + sstube=1.0d0 + ssgradtube=0.0d0 + enetube(i+nres)=enetube(i+nres)+sstube*tubetranene(itype(i)) +C print *,"I am in true lipid" + endif + else +C sstube=0.0d0 +C ssgradtube=0.0d0 + cycle + endif ! if in lipid or buffor +CEND OF FINITE FRAGMENT +C as the tube is infinity we do not calculate the Z-vector use of Z +C as chosen axis + vectube(3)=0.0d0 +C now calculte the distance + tub_r=dsqrt(vectube(1)**2+vectube(2)**2+vectube(3)**2) +C now normalize vector + vectube(1)=vectube(1)/tub_r + vectube(2)=vectube(2)/tub_r +C calculte rdiffrence between r and r0 + rdiff=tub_r-tubeR0 +C and its 6 power + rdiff6=rdiff**6.0d0 +C for vectorization reasons we will sumup at the end to avoid depenence of previous + sc_aa_tube=sc_aa_tube_par(iti) + sc_bb_tube=sc_bb_tube_par(iti) + enetube(i+nres)=(sc_aa_tube/rdiff6**2.0d0+sc_bb_tube/rdiff6) + & *sstube+enetube(i+nres) +C pep_aa_tube and pep_bb_tube are precomputed values A=4eps*sigma^12 B=4eps*sigma^6 +C now we calculate gradient + fac=(-12.0d0*sc_aa_tube/rdiff6**2.0d0/rdiff- + & 6.0d0*sc_bb_tube/rdiff6/rdiff)*sstube +C now direction of gg_tube vector + do j=1,3 + gg_tube_SC(j,i)=gg_tube_SC(j,i)+vectube(j)*fac + gg_tube(j,i-1)=gg_tube(j,i-1)+vectube(j)*fac + enddo + gg_tube_SC(3,i)=gg_tube_SC(3,i) + &+ssgradtube*enetube(i+nres)/sstube + gg_tube(3,i-1)= gg_tube(3,i-1) + &+ssgradtube*enetube(i+nres)/sstube + + enddo + do i=itube_start,itube_end + Etube=Etube+enetube(i)+enetube(i+nres) + enddo +C print *,"ETUBE", etube + return + end +C TO DO 1) add to total energy +C 2) add to gradient summation +C 3) add reading parameters (AND of course oppening of PARAM file) +C 4) add reading the center of tube +C 5) add COMMONs +C 6) add to zerograd + + +C#------------------------------------------------------------------------------- +C This subroutine is to mimic the histone like structure but as well can be +C utilizet to nanostructures (infinit) small modification has to be used to +C make it finite (z gradient at the ends has to be changes as well as the x,y +C gradient has to be modified at the ends +C The energy function is Kihara potential +C E=4esp*((sigma/(r-r0))^12 - (sigma/(r-r0))^6) +C 4eps is depth of well sigma is r_minimum r is distance from center of tube +C and r0 is the excluded size of nanotube (can be set to 0 if we want just a +C simple Kihara potential + subroutine calcnano(Etube) + 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.NAMES' + include 'COMMON.INTERACT' + include 'COMMON.IOUNITS' + include 'COMMON.CALC' + include 'COMMON.CONTROL' + include 'COMMON.SPLITELE' + include 'COMMON.SBRIDGE' + double precision tub_r,vectube(3),enetube(maxres*2), + & enecavtube(maxres*2) + Etube=0.0d0 + do i=itube_start,itube_end + enetube(i)=0.0d0 + enetube(i+nres)=0.0d0 + enddo +C first we calculate the distance from tube center +C first sugare-phosphate group for NARES this would be peptide group +C for UNRES + do i=itube_start,itube_end +C lets ommit dummy atoms for now + if ((itype(i).eq.ntyp1).or.(itype(i+1).eq.ntyp1)) cycle +C now calculate distance from center of tube and direction vectors + xmin=boxxsize + ymin=boxysize + zmin=boxzsize + + do j=-1,1 + vectube(1)=dmod((c(1,i)+c(1,i+1))/2.0d0,boxxsize) + vectube(1)=vectube(1)+boxxsize*j + vectube(2)=dmod((c(2,i)+c(2,i+1))/2.0d0,boxysize) + vectube(2)=vectube(2)+boxysize*j + vectube(3)=dmod((c(3,i)+c(3,i+1))/2.0d0,boxzsize) + vectube(3)=vectube(3)+boxzsize*j + + + xminact=dabs(vectube(1)-tubecenter(1)) + yminact=dabs(vectube(2)-tubecenter(2)) + zminact=dabs(vectube(3)-tubecenter(3)) + + if (xmin.gt.xminact) then + xmin=xminact + xtemp=vectube(1) + endif + if (ymin.gt.yminact) then + ymin=yminact + ytemp=vectube(2) + endif + if (zmin.gt.zminact) then + zmin=zminact + ztemp=vectube(3) + endif + enddo + vectube(1)=xtemp + vectube(2)=ytemp + vectube(3)=ztemp + + vectube(1)=vectube(1)-tubecenter(1) + vectube(2)=vectube(2)-tubecenter(2) + vectube(3)=vectube(3)-tubecenter(3) + +C print *,"x",(c(1,i)+c(1,i+1))/2.0d0,tubecenter(1) +C print *,"y",(c(2,i)+c(2,i+1))/2.0d0,tubecenter(2) +C as the tube is infinity we do not calculate the Z-vector use of Z +C as chosen axis +C vectube(3)=0.0d0 +C now calculte the distance + tub_r=dsqrt(vectube(1)**2+vectube(2)**2+vectube(3)**2) +C now normalize vector + vectube(1)=vectube(1)/tub_r + vectube(2)=vectube(2)/tub_r + vectube(3)=vectube(3)/tub_r +C calculte rdiffrence between r and r0 + rdiff=tub_r-tubeR0 +C and its 6 power + rdiff6=rdiff**6.0d0 +C for vectorization reasons we will sumup at the end to avoid depenence of previous + enetube(i)=pep_aa_tube/rdiff6**2.0d0+pep_bb_tube/rdiff6 +C write(iout,*) "TU13",i,rdiff6,enetube(i) +C print *,rdiff,rdiff6,pep_aa_tube +C pep_aa_tube and pep_bb_tube are precomputed values A=4eps*sigma^12 B=4eps*sigma^6 +C now we calculate gradient + fac=(-12.0d0*pep_aa_tube/rdiff6- + & 6.0d0*pep_bb_tube)/rdiff6/rdiff +C write(iout,'(a5,i4,f12.1,3f12.5)') "TU13",i,rdiff6,enetube(i), +C &rdiff,fac + if (acavtubpep.eq.0.0d0) then +C go to 667 + enecavtube(i)=0.0 + faccav=0.0 + else + denominator=(1.0d0+dcavtubpep*rdiff6*rdiff6) + enecavtube(i)= + & (bcavtubpep*rdiff+acavtubpep*dsqrt(rdiff)+ccavtubpep) + & /denominator + enecavtube(i)=0.0 + faccav=((bcavtubpep*1.0d0+acavtubpep/2.0d0/dsqrt(rdiff)) + & *denominator-(bcavtubpep*rdiff+acavtubpep*dsqrt(rdiff) + & +ccavtubpep)*rdiff6**2.0d0/rdiff*dcavtubpep*12.0d0) + & /denominator**2.0d0 +C faccav=0.0 +C fac=fac+faccav +C 667 continue + endif +C print *,"TUT",i,iti,rdiff,rdiff6,acavtubpep,denominator, +C & enecavtube(i),faccav +C print *,"licz=", +C & (bcavtub(iti)*rdiff+acavtub(iti)*sqrt(rdiff)+ccavtub(iti)) +CX print *,"finene=",enetube(i+nres)+enecavtube(i) + +C now direction of gg_tube vector + do j=1,3 + gg_tube(j,i-1)=gg_tube(j,i-1)+vectube(j)*fac/2.0d0 + gg_tube(j,i)=gg_tube(j,i)+vectube(j)*fac/2.0d0 + enddo + enddo + + do i=itube_start,itube_end + enecavtube(i)=0.0d0 +C Lets not jump over memory as we use many times iti + iti=itype(i) +C lets ommit dummy atoms for now + if ((iti.eq.ntyp1) +C in UNRES uncomment the line below as GLY has no side-chain... +C .or.(iti.eq.10) + & ) cycle + xmin=boxxsize + ymin=boxysize + zmin=boxzsize + do j=-1,1 + vectube(1)=dmod((c(1,i+nres)),boxxsize) + vectube(1)=vectube(1)+boxxsize*j + vectube(2)=dmod((c(2,i+nres)),boxysize) + vectube(2)=vectube(2)+boxysize*j + vectube(3)=dmod((c(3,i+nres)),boxzsize) + vectube(3)=vectube(3)+boxzsize*j + + + xminact=dabs(vectube(1)-tubecenter(1)) + yminact=dabs(vectube(2)-tubecenter(2)) + zminact=dabs(vectube(3)-tubecenter(3)) + + if (xmin.gt.xminact) then + xmin=xminact + xtemp=vectube(1) + endif + if (ymin.gt.yminact) then + ymin=yminact + ytemp=vectube(2) + endif + if (zmin.gt.zminact) then + zmin=zminact + ztemp=vectube(3) + endif + enddo + vectube(1)=xtemp + vectube(2)=ytemp + vectube(3)=ztemp + +C write(iout,*), "tututu", vectube(1),tubecenter(1),vectube(2), +C & tubecenter(2) + vectube(1)=vectube(1)-tubecenter(1) + vectube(2)=vectube(2)-tubecenter(2) + vectube(3)=vectube(3)-tubecenter(3) +C now calculte the distance + tub_r=dsqrt(vectube(1)**2+vectube(2)**2+vectube(3)**2) +C now normalize vector + vectube(1)=vectube(1)/tub_r + vectube(2)=vectube(2)/tub_r + vectube(3)=vectube(3)/tub_r + +C calculte rdiffrence between r and r0 + rdiff=tub_r-tubeR0 +C and its 6 power + rdiff6=rdiff**6.0d0 +C for vectorization reasons we will sumup at the end to avoid depenence of previous + sc_aa_tube=sc_aa_tube_par(iti) + sc_bb_tube=sc_bb_tube_par(iti) + enetube(i+nres)=sc_aa_tube/rdiff6**2.0d0+sc_bb_tube/rdiff6 +C enetube(i+nres)=0.0d0 +C pep_aa_tube and pep_bb_tube are precomputed values A=4eps*sigma^12 B=4eps*sigma^6 +C now we calculate gradient + fac=-12.0d0*sc_aa_tube/rdiff6**2.0d0/rdiff- + & 6.0d0*sc_bb_tube/rdiff6/rdiff +C fac=0.0 +C now direction of gg_tube vector +C Now cavity term E=a(x+bsqrt(x)+c)/(1+dx^12) + if (acavtub(iti).eq.0.0d0) then +C go to 667 + enecavtube(i+nres)=0.0d0 + faccav=0.0d0 + else + denominator=(1.0d0+dcavtub(iti)*rdiff6*rdiff6) + enecavtube(i+nres)= + & (bcavtub(iti)*rdiff+acavtub(iti)*dsqrt(rdiff)+ccavtub(iti)) + & /denominator +C enecavtube(i)=0.0 + faccav=((bcavtub(iti)*1.0d0+acavtub(iti)/2.0d0/dsqrt(rdiff)) + & *denominator-(bcavtub(iti)*rdiff+acavtub(iti)*dsqrt(rdiff) + & +ccavtub(iti))*rdiff6**2.0d0/rdiff*dcavtub(iti)*12.0d0) + & /denominator**2.0d0 +C faccav=0.0 + fac=fac+faccav +C 667 continue + endif +C print *,"TUT",i,iti,rdiff,rdiff6,acavtub(iti),denominator, +C & enecavtube(i),faccav +C print *,"licz=", +C & (bcavtub(iti)*rdiff+acavtub(iti)*sqrt(rdiff)+ccavtub(iti)) +C print *,"finene=",enetube(i+nres)+enecavtube(i) + do j=1,3 + gg_tube_SC(j,i)=gg_tube_SC(j,i)+vectube(j)*fac + gg_tube(j,i-1)=gg_tube(j,i-1)+vectube(j)*fac + enddo + enddo +C Now cavity term E=a(x+bsqrt(x)+c)/(1+dx^12) +C do i=itube_start,itube_end +C enecav(i)=0.0 +C iti=itype(i) +C if (acavtub(iti).eq.0.0) cycle + + + + do i=itube_start,itube_end + Etube=Etube+enetube(i)+enetube(i+nres)+enecavtube(i) + & +enecavtube(i+nres) + enddo +C print *,"ETUBE", etube + return + end +C TO DO 1) add to total energy +C 2) add to gradient summation +C 3) add reading parameters (AND of course oppening of PARAM file) +C 4) add reading the center of tube +C 5) add COMMONs +C 6) add to zerograd