include 'COMMON.MD'
include 'COMMON.CONTROL'
include 'COMMON.TIME1'
+ include 'COMMON.SPLITELE'
+ include 'COMMON.TORCNSTR'
#ifdef MPI
c print*,"ETOTAL Processor",fg_rank," absolute rank",myrank,
c & " nfgtasks",nfgtasks
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)
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
C
C Compute the side-chain and electrostatic interaction energy
C
+C print *,ipot
goto (101,102,103,104,105,106) ipot
C Lennard-Jones potential.
101 call elj(evdw)
goto 107
C Gay-Berne potential (shifted LJ, angular dependence).
104 call egb(evdw)
+C print *,"bylem w egb"
goto 107
C Gay-Berne-Vorobjev potential (shifted LJ, angular dependence).
105 call egbv(evdw)
C Calculate electrostatic (H-bonding) energy of the main chain.
C
107 continue
+cmc
+cmc Sep-06: egb takes care of dynamic ss bonds too
+cmc
+c if (dyn_ss) call dyn_set_nss
+
c print *,"Processor",myrank," computed USCSC"
#ifdef TIMING
time01=MPI_Wtime()
#ifdef TIMING
time_vec=time_vec+MPI_Wtime()-time01
#endif
+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
+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
+ endif
c print *,"Processor",myrank," left VEC_AND_DERIV"
if (ipot.lt.6) then
#ifdef SPLITELE
eello_turn4=0.0d0
endif
else
-c write (iout,*) "Soft-spheer ELEC potential"
- call eelec_soft_sphere(ees,evdw1,eel_loc,eello_turn3,
- & eello_turn4)
+ write (iout,*) "Soft-spheer ELEC potential"
+c call eelec_soft_sphere(ees,evdw1,eel_loc,eello_turn3,
+c & eello_turn4)
endif
c print *,"Processor",myrank," computed UELEC"
C
C Calculate the virtual-bond-angle energy.
C
if (wang.gt.0d0) then
- call ebend(ebe)
+ if (tor_mode.eq.0) then
+ call ebend(ebe)
+ else
+C ebend kcc is Kubo cumulant clustered rigorous attemp to derive the
+C energy function
+ call ebend_kcc(ebe)
+ endif
else
- ebe=0
+ ebe=0.0d0
endif
+ ethetacnstr=0.0d0
+ if (with_theta_constr) call etheta_constr(ethetacnstr)
c print *,"Processor",myrank," computed UB"
C
C Calculate the SC local energy.
C
+C print *,"TU DOCHODZE?"
call esc(escloc)
c print *,"Processor",myrank," computed USC"
C
C Calculate the virtual-bond torsional energy.
C
cd print *,'nterm=',nterm
- if (wtor.gt.0) then
- call etor(etors,edihcnstr)
+C print *,"tor",tor_mode
+ if (wtor.gt.0.0d0) then
+ if (tor_mode.eq.0) then
+ call etor(etors)
+ else
+C etor kcc is Kubo cumulant clustered rigorous attemp to derive the
+C energy function
+ call etor_kcc(etors)
+ endif
else
- etors=0
- edihcnstr=0
+ etors=0.0d0
endif
+ edihcnstr=0.0d0
+ if (ndih_constr.gt.0) call etor_constr(edihcnstr)
c print *,"Processor",myrank," computed Utor"
C
C 6/23/01 Calculate double-torsional energy
C
- if (wtor_d.gt.0) then
- call etor_d(etors_d)
+ if ((wtor_d.gt.0.0d0).and.(tor_mode.eq.0)) then
+ call etor_d(etors_d)
else
- etors_d=0
+ etors_d=0
endif
c print *,"Processor",myrank," computed Utord"
C
else
esccor=0.0d0
endif
+C print *,"PRZED MULIt"
c print *,"Processor",myrank," computed Usccorr"
C
C 12/1/95 Multi-body terms
if ((wcorr4.gt.0.0d0 .or. wcorr5.gt.0.0d0 .or. wcorr6.gt.0.0d0
& .or. wturn6.gt.0.0d0) .and. ipot.lt.6) then
call multibody_eello(ecorr,ecorr5,ecorr6,eturn6,n_corr,n_corr1)
-cd write(2,*)'multibody_eello n_corr=',n_corr,' n_corr1=',n_corr1,
-cd &" ecorr",ecorr," ecorr5",ecorr5," ecorr6",ecorr6," eturn6",eturn6
+c write(2,*)'MULTIBODY_EELLO n_corr=',n_corr,' n_corr1=',n_corr1,
+c &" ecorr",ecorr," ecorr5",ecorr5," ecorr6",ecorr6," eturn6",eturn6
+c call flush(iout)
else
ecorr=0.0d0
ecorr5=0.0d0
eturn6=0.0d0
endif
if ((wcorr4.eq.0.0d0 .and. wcorr.gt.0.0d0) .and. ipot.lt.6) then
+c write (iout,*) "Before MULTIBODY_HB ecorr",ecorr,ecorr5,ecorr6,
+c & n_corr,n_corr1
+c call flush(iout)
call multibody_hb(ecorr,ecorr5,ecorr6,n_corr,n_corr1)
-cd write (iout,*) "multibody_hb ecorr",ecorr
+c write (iout,*) "MULTIBODY_HB ecorr",ecorr,ecorr5,ecorr6,n_corr,
+c & n_corr1
+c call flush(iout)
endif
c print *,"Processor",myrank," computed Ucorr"
C
C If performing constraint dynamics, call the constraint energy
C after the equilibration time
- if(usampl.and.totT.gt.eq_time) then
+c if(usampl.and.totT.gt.eq_time) then
+c write (iout,*) "usampl",usampl
+ if(usampl) then
call EconstrQ
- call Econstr_back
+ if (loc_qlike) then
+ call Econstr_back_qlike
+ else
+ call Econstr_back
+ endif
else
Uconst=0.0d0
Uconst_back=0.0d0
endif
+C 01/27/2015 added by adasko
+C the energy component below is energy transfer into lipid environment
+C based on partition function
+C print *,"przed lipidami"
+ if (wliptran.gt.0) then
+ call Eliptransfer(eliptran)
+ endif
+C print *,"za lipidami"
+ if (AFMlog.gt.0) then
+ call AFMforce(Eafmforce)
+ 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)
+ else
+ Etube=0.0d0
+ endif
+
#ifdef TIMING
time_enecalc=time_enecalc+MPI_Wtime()-time00
#endif
energia(17)=estr
energia(20)=Uconst+Uconst_back
energia(21)=esccor
+ 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"
call sum_energy(energia,.true.)
+ if (dyn_ss) call dyn_set_nss
c print *," Processor",myrank," left SUM_ENERGY"
#ifdef TIMING
time_sumene=time_sumene+MPI_Wtime()-time00
estr=energia(17)
Uconst=energia(20)
esccor=energia(21)
+ 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
& +wstrain*ehpb+wcorr*ecorr+wcorr5*ecorr5
& +wcorr6*ecorr6+wturn4*eello_turn4+wturn3*eello_turn3
& +wturn6*eturn6+wel_loc*eel_loc+edihcnstr+wtor_d*etors_d
- & +wbond*estr+Uconst+wsccor*esccor
+ & +wbond*estr+wumb*Uconst+wsccor*esccor+wliptran*eliptran+Eafmforce
+ & +ethetacnstr+wtube*Etube
#else
etot=wsc*evdw+wscp*evdw2+welec*(ees+evdw1)
& +wang*ebe+wtor*etors+wscloc*escloc
& +wstrain*ehpb+wcorr*ecorr+wcorr5*ecorr5
& +wcorr6*ecorr6+wturn4*eello_turn4+wturn3*eello_turn3
& +wturn6*eturn6+wel_loc*eel_loc+edihcnstr+wtor_d*etors_d
- & +wbond*estr+Uconst+wsccor*esccor
+ & +wbond*estr+wumb*Uconst+wsccor*esccor+wliptran*eliptran
+ & +Eafmforce
+ & +ethetacnstr+wtube*Etube
#endif
energia(0)=etot
c detecting NaNQ
#endif
#ifdef MPI
include 'mpif.h'
- double precision gradbufc(3,maxres),gradbufx(3,maxres),
- & glocbuf(4*maxres),gradbufc_sum(3,maxres)
#endif
+ double precision gradbufc(3,-1:maxres),gradbufx(3,-1:maxres),
+ & glocbuf(4*maxres),gradbufc_sum(3,-1:maxres)
+ & ,gloc_scbuf(3,-1:maxres)
include 'COMMON.SETUP'
include 'COMMON.IOUNITS'
include 'COMMON.FFIELD'
include 'COMMON.CONTROL'
include 'COMMON.TIME1'
include 'COMMON.MAXGRAD'
+ include 'COMMON.SCCOR'
#ifdef TIMING
time01=MPI_Wtime()
#endif
call flush(iout)
#endif
#ifdef SPLITELE
- do i=1,nct
+ do i=0,nct
do j=1,3
gradbufc(j,i)=wsc*gvdwc(j,i)+
& wscp*(gvdwc_scp(j,i)+gvdwc_scpp(j,i))+
& wcorr6*gradcorr6_long(j,i)+
& wturn6*gcorr6_turn_long(j,i)+
& 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
#else
- do i=1,nct
+ do i=0,nct
do j=1,3
gradbufc(j,i)=wsc*gvdwc(j,i)+
& wscp*(gvdwc_scp(j,i)+gvdwc_scpp(j,i))+
& wcorr6*gradcorr6_long(j,i)+
& wturn6*gcorr6_turn_long(j,i)+
& 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
#endif
enddo
call flush(iout)
#endif
- do i=1,nres
+ do i=0,nres
do j=1,3
gradbufc_sum(j,i)=gradbufc(j,i)
enddo
do j=1,3
gradbufc(j,nres-1)=gradbufc_sum(j,nres)
enddo
- do i=nres-2,nnt,-1
+ do i=nres-2,-1,-1
do j=1,3
gradbufc(j,i)=gradbufc(j,i+1)+gradbufc_sum(j,i+1)
enddo
enddo
call flush(iout)
#endif
- do i=1,nres
+ do i=-1,nres
do j=1,3
gradbufc_sum(j,i)=gradbufc(j,i)
gradbufc(j,i)=0.0d0
do j=1,3
gradbufc(j,nres-1)=gradbufc_sum(j,nres)
enddo
- do i=nres-2,nnt,-1
+ do i=nres-2,-1,-1
do j=1,3
gradbufc(j,i)=gradbufc(j,i+1)+gradbufc_sum(j,i+1)
enddo
do k=1,3
gradbufc(k,nres)=0.0d0
enddo
- do i=1,nct
+ 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)+
& wturn6*gcorr6_turn(j,i)+
& wsccor*gsccorc(j,i)
& +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)+
& wturn6*gcorr6_turn(j,i)+
& wsccor*gsccorc(j,i)
& +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)+
& wbond*gradbx(j,i)+
& wstrain*ghpbx(j,i)+wcorr*gradxorr(j,i)+
& 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
#ifdef DEBUG
& +wturn3*gel_loc_turn3(i)
& +wturn6*gel_loc_turn6(i)
& +wel_loc*gel_loc_loc(i)
- & +wsccor*gsccor_loc(i)
enddo
#ifdef DEBUG
write (iout,*) "gloc after adding corr"
do i=1,4*nres
glocbuf(i)=gloc(i,icg)
enddo
+c#define DEBUG
+#ifdef DEBUG
+ write (iout,*) "gloc_sc before reduce"
+ do i=1,nres
+ do j=1,1
+ write (iout,*) i,j,gloc_sc(j,i,icg)
+ enddo
+ enddo
+#endif
+c#undef DEBUG
+ do i=1,nres
+ do j=1,3
+ gloc_scbuf(j,i)=gloc_sc(j,i,icg)
+ enddo
+ enddo
time00=MPI_Wtime()
call MPI_Barrier(FG_COMM,IERR)
time_barrier_g=time_barrier_g+MPI_Wtime()-time00
call MPI_Reduce(glocbuf(1),gloc(1,icg),4*nres,
& MPI_DOUBLE_PRECISION,MPI_SUM,king,FG_COMM,IERR)
time_reduce=time_reduce+MPI_Wtime()-time00
+ call MPI_Reduce(gloc_scbuf(1,1),gloc_sc(1,1,icg),3*nres,
+ & MPI_DOUBLE_PRECISION,MPI_SUM,king,FG_COMM,IERR)
+ time_reduce=time_reduce+MPI_Wtime()-time00
+c#define DEBUG
+#ifdef DEBUG
+ write (iout,*) "gloc_sc after reduce"
+ do i=1,nres
+ do j=1,1
+ write (iout,*) i,j,gloc_sc(j,i,icg)
+ enddo
+ enddo
+#endif
+c#undef DEBUG
#ifdef DEBUG
write (iout,*) "gloc after reduce"
do i=1,4*nres
if (gsclocx_norm.gt.gsclocx_max) gsclocx_max=gsclocx_norm
enddo
if (gradout) then
-#ifdef AIX
+#if (defined AIX || defined CRAY)
open(istat,file=statname,position="append")
#else
open(istat,file=statname,access="append")
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
#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
wtor=weights(13)*fact
wtor_d=weights(14)*fact2
wsccor=weights(21)*fact
+ if (scale_umb) wumb=t_bath/temp0
+c write (iout,*) "scale_umb",scale_umb
+c write (iout,*) "t_bath",t_bath," temp0",temp0," wumb",wumb
return
end
estr=energia(17)
Uconst=energia(20)
esccor=energia(21)
+ 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,wsccor,
- & edihcnstr,ebr*nss,
- & Uconst,etot
+ & 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)'/
& 'EVDW2= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-p)'/
& 'ETURN6=',1pE16.6,' WEIGHT=',1pD16.6,' (turns, 6th order)'/
& 'ESCCOR=',1pE16.6,' WEIGHT=',1pD16.6,' (backbone-rotamer corr)'/
& 'EDIHC= ',1pE16.6,' (dihedral angle constraints)'/
+ & 'ETHETC= ',1pE16.6,' (valence angle constraints)'/
& 'ESS= ',1pE16.6,' (disulfide-bridge intrinsic energy)'/
& '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
write (iout,10) evdw,wsc,evdw2,wscp,ees,welec,
& estr,wbond,ebe,wang,
& ecorr,wcorr,
& ecorr5,wcorr5,ecorr6,wcorr6,eel_loc,wel_loc,eello_turn3,wturn3,
& eello_turn4,wturn4,eello_turn6,wturn6,esccor,wsccro,edihcnstr,
- & ebr*nss,Uconst,etot
+ & ethetacnstr,ebr*nss,Uconst,eliptran,wliptran,Eafmforc,
+ & etube,wtube,
+ & etot
10 format (/'Virtual-chain energies:'//
& 'EVDW= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-SC)'/
& 'EVDW2= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-p)'/
& 'ETURN6=',1pE16.6,' WEIGHT=',1pD16.6,' (turns, 6th order)'/
& 'ESCCOR=',1pE16.6,' WEIGHT=',1pD16.6,' (backbone-rotamer corr)'/
& 'EDIHC= ',1pE16.6,' (dihedral angle constraints)'/
+ & 'ETHETC= ',1pE16.6,' (valence angle constraints)'/
& 'ESS= ',1pE16.6,' (disulfide-bridge intrinsic energy)'/
& '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
c write(iout,*)'Entering ELJ nnt=',nnt,' nct=',nct,' expon=',expon
evdw=0.0D0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- if (itypi.eq.21) cycle
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ if (itypi.eq.ntyp1) cycle
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
cd write (iout,*) 'i=',i,' iint=',iint,' istart=',istart(i,iint),
cd & 'iend=',iend(i,iint)
do j=istart(i,iint),iend(i,iint)
- itypj=itype(j)
- if (itypj.eq.21) cycle
+ itypj=iabs(itype(j))
+ if (itypj.eq.ntyp1) cycle
xj=c(1,nres+j)-xi
yj=c(2,nres+j)-yi
zj=c(3,nres+j)-zi
c write (iout,*)'i=',i,' j=',j,' itypi=',itypi,' itypj=',itypj
eps0ij=eps(itypi,itypj)
fac=rrij**expon2
- e1=fac*fac*aa(itypi,itypj)
- e2=fac*bb(itypi,itypj)
+C have you changed here?
+ e1=fac*fac*aa
+ e2=fac*bb
evdwij=e1+e2
cd sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
cd epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
cd write (iout,'(2(a3,i3,2x),6(1pd12.4)/2(3(1pd12.4),5x)/)')
-cd & restyp(itypi),i,restyp(itypj),j,aa(itypi,itypj),
+cd & restyp(itypi),i,restyp(itypj),j,a(itypi,itypj),
cd & bb(itypi,itypj),1.0D0/dsqrt(rrij),evdwij,epsi,sigm,
cd & (c(k,i),k=1,3),(c(k,j),k=1,3)
evdw=evdw+evdwij
c print *,'Entering ELJK nnt=',nnt,' nct=',nct,' expon=',expon
evdw=0.0D0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- if (itypi.eq.21) cycle
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ if (itypi.eq.ntyp1) cycle
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
C
do iint=1,nint_gr(i)
do j=istart(i,iint),iend(i,iint)
- itypj=itype(j)
- if (itypj.eq.21) cycle
+ itypj=iabs(itype(j))
+ if (itypj.eq.ntyp1) cycle
xj=c(1,nres+j)-xi
yj=c(2,nres+j)-yi
zj=c(3,nres+j)-zi
rij=1.0D0/r_inv_ij
r_shift_inv=1.0D0/(rij+r0(itypi,itypj)-sigma(itypi,itypj))
fac=r_shift_inv**expon
- e1=fac*fac*aa(itypi,itypj)
- e2=fac*bb(itypi,itypj)
+C have you changed here?
+ e1=fac*fac*aa
+ e2=fac*bb
evdwij=e_augm+e1+e2
cd sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
cd epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
c endif
ind=0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- if (itypi.eq.21) cycle
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ if (itypi.eq.ntyp1) cycle
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
do iint=1,nint_gr(i)
do j=istart(i,iint),iend(i,iint)
ind=ind+1
- itypj=itype(j)
- if (itypj.eq.21) cycle
+ itypj=iabs(itype(j))
+ if (itypj.eq.ntyp1) cycle
c dscj_inv=dsc_inv(itypj)
dscj_inv=vbld_inv(j+nres)
chi1=chi(itypi,itypj)
call sc_angular
C Calculate whole angle-dependent part of epsilon and contributions
C to its derivatives
+C have you changed here?
fac=(rrij*sigsq)**expon2
- e1=fac*fac*aa(itypi,itypj)
- e2=fac*bb(itypi,itypj)
+ e1=fac*fac*aa
+ e2=fac*bb
evdwij=eps1*eps2rt*eps3rt*(e1+e2)
eps2der=evdwij*eps3rt
eps3der=evdwij*eps2rt
evdwij=evdwij*eps2rt*eps3rt
evdw=evdw+evdwij
if (lprn) then
- sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
- epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
+ sigm=dabs(aa/bb)**(1.0D0/6.0D0)
+ epsi=bb**2/aa
cd write (iout,'(2(a3,i3,2x),15(0pf7.3))')
cd & restyp(itypi),i,restyp(itypj),j,
cd & epsi,sigm,chi1,chi2,chip1,chip2,
include 'COMMON.IOUNITS'
include 'COMMON.CALC'
include 'COMMON.CONTROL'
+ include 'COMMON.SPLITELE'
+ include 'COMMON.SBRIDGE'
logical lprn
+ integer xshift,yshift,zshift
+
evdw=0.0D0
ccccc energy_dec=.false.
-c print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon
+C print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon
evdw=0.0D0
lprn=.false.
c if (icall.eq.0) lprn=.false.
ind=0
+C the loop over all 27 posible neigbours (for xshift=0,yshift=0,zshift=0
+C we have the original box)
+C do xshift=-1,1
+C do yshift=-1,1
+C do zshift=-1,1
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- if (itypi.eq.21) cycle
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ if (itypi.eq.ntyp1) cycle
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
+C Return atom into box, boxxsize is size of box in x dimension
+c 134 continue
+c if (xi.gt.((xshift+0.5d0)*boxxsize)) xi=xi-boxxsize
+c if (xi.lt.((xshift-0.5d0)*boxxsize)) xi=xi+boxxsize
+C Condition for being inside the proper box
+c if ((xi.gt.((xshift+0.5d0)*boxxsize)).or.
+c & (xi.lt.((xshift-0.5d0)*boxxsize))) then
+c go to 134
+c endif
+c 135 continue
+c if (yi.gt.((yshift+0.5d0)*boxysize)) yi=yi-boxysize
+c if (yi.lt.((yshift-0.5d0)*boxysize)) yi=yi+boxysize
+C Condition for being inside the proper box
+c if ((yi.gt.((yshift+0.5d0)*boxysize)).or.
+c & (yi.lt.((yshift-0.5d0)*boxysize))) then
+c go to 135
+c endif
+c 136 continue
+c if (zi.gt.((zshift+0.5d0)*boxzsize)) zi=zi-boxzsize
+c if (zi.lt.((zshift-0.5d0)*boxzsize)) zi=zi+boxzsize
+C Condition for being inside the proper box
+c if ((zi.gt.((zshift+0.5d0)*boxzsize)).or.
+c & (zi.lt.((zshift-0.5d0)*boxzsize))) then
+c go to 136
+c endif
+ xi=mod(xi,boxxsize)
+ if (xi.lt.0) xi=xi+boxxsize
+ yi=mod(yi,boxysize)
+ if (yi.lt.0) yi=yi+boxysize
+ zi=mod(zi,boxzsize)
+ if (zi.lt.0) zi=zi+boxzsize
+C define scaling factor for lipids
+
+C if (positi.le.0) positi=positi+boxzsize
+C print *,i
+C first for peptide groups
+c for each residue check if it is in lipid or lipid water border area
+ if ((zi.gt.bordlipbot)
+ &.and.(zi.lt.bordliptop)) then
+C the energy transfer exist
+ if (zi.lt.buflipbot) then
+C what fraction I am in
+ fracinbuf=1.0d0-
+ & ((zi-bordlipbot)/lipbufthick)
+C lipbufthick is thickenes of lipid buffore
+ sslipi=sscalelip(fracinbuf)
+ ssgradlipi=-sscagradlip(fracinbuf)/lipbufthick
+ elseif (zi.gt.bufliptop) then
+ fracinbuf=1.0d0-((bordliptop-zi)/lipbufthick)
+ sslipi=sscalelip(fracinbuf)
+ ssgradlipi=sscagradlip(fracinbuf)/lipbufthick
+ else
+ sslipi=1.0d0
+ ssgradlipi=0.0
+ endif
+ else
+ sslipi=0.0d0
+ ssgradlipi=0.0
+ endif
+
+C xi=xi+xshift*boxxsize
+C yi=yi+yshift*boxysize
+C zi=zi+zshift*boxzsize
+
dxi=dc_norm(1,nres+i)
dyi=dc_norm(2,nres+i)
dzi=dc_norm(3,nres+i)
C
do iint=1,nint_gr(i)
do j=istart(i,iint),iend(i,iint)
+ IF (dyn_ss_mask(i).and.dyn_ss_mask(j)) THEN
+
+c write(iout,*) "PRZED ZWYKLE", evdwij
+ call dyn_ssbond_ene(i,j,evdwij)
+c write(iout,*) "PO ZWYKLE", evdwij
+
+ evdw=evdw+evdwij
+ if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a3)')
+ & 'evdw',i,j,evdwij,' ss'
+C triple bond artifac removal
+ do k=j+1,iend(i,iint)
+C search over all next residues
+ if (dyn_ss_mask(k)) then
+C check if they are cysteins
+C write(iout,*) 'k=',k
+
+c write(iout,*) "PRZED TRI", evdwij
+ evdwij_przed_tri=evdwij
+ call triple_ssbond_ene(i,j,k,evdwij)
+c if(evdwij_przed_tri.ne.evdwij) then
+c write (iout,*) "TRI:", evdwij, evdwij_przed_tri
+c endif
+
+c write(iout,*) "PO TRI", evdwij
+C call the energy function that removes the artifical triple disulfide
+C bond the soubroutine is located in ssMD.F
+ evdw=evdw+evdwij
+ if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a3)')
+ & 'evdw',i,j,evdwij,'tss'
+ endif!dyn_ss_mask(k)
+ enddo! k
+ ELSE
ind=ind+1
- itypj=itype(j)
- if (itypj.eq.21) cycle
+ itypj=iabs(itype(j))
+ if (itypj.eq.ntyp1) cycle
c dscj_inv=dsc_inv(itypj)
dscj_inv=vbld_inv(j+nres)
c write (iout,*) "j",j,dsc_inv(itypj),dscj_inv,
c alf1=0.0D0
c alf2=0.0D0
c alf12=0.0D0
- xj=c(1,nres+j)-xi
- yj=c(2,nres+j)-yi
- zj=c(3,nres+j)-zi
+ xj=c(1,nres+j)
+ yj=c(2,nres+j)
+ zj=c(3,nres+j)
+C Return atom J into box the original box
+c 137 continue
+c if (xj.gt.((0.5d0)*boxxsize)) xj=xj-boxxsize
+c if (xj.lt.((-0.5d0)*boxxsize)) xj=xj+boxxsize
+C Condition for being inside the proper box
+c if ((xj.gt.((0.5d0)*boxxsize)).or.
+c & (xj.lt.((-0.5d0)*boxxsize))) then
+c go to 137
+c endif
+c 138 continue
+c if (yj.gt.((0.5d0)*boxysize)) yj=yj-boxysize
+c if (yj.lt.((-0.5d0)*boxysize)) yj=yj+boxysize
+C Condition for being inside the proper box
+c if ((yj.gt.((0.5d0)*boxysize)).or.
+c & (yj.lt.((-0.5d0)*boxysize))) then
+c go to 138
+c endif
+c 139 continue
+c if (zj.gt.((0.5d0)*boxzsize)) zj=zj-boxzsize
+c if (zj.lt.((-0.5d0)*boxzsize)) zj=zj+boxzsize
+C Condition for being inside the proper box
+c if ((zj.gt.((0.5d0)*boxzsize)).or.
+c & (zj.lt.((-0.5d0)*boxzsize))) then
+c go to 139
+c endif
+ xj=mod(xj,boxxsize)
+ if (xj.lt.0) xj=xj+boxxsize
+ yj=mod(yj,boxysize)
+ if (yj.lt.0) yj=yj+boxysize
+ zj=mod(zj,boxzsize)
+ if (zj.lt.0) zj=zj+boxzsize
+ if ((zj.gt.bordlipbot)
+ &.and.(zj.lt.bordliptop)) then
+C the energy transfer exist
+ if (zj.lt.buflipbot) then
+C what fraction I am in
+ fracinbuf=1.0d0-
+ & ((zj-bordlipbot)/lipbufthick)
+C lipbufthick is thickenes of lipid buffore
+ sslipj=sscalelip(fracinbuf)
+ ssgradlipj=-sscagradlip(fracinbuf)/lipbufthick
+ elseif (zj.gt.bufliptop) then
+ fracinbuf=1.0d0-((bordliptop-zj)/lipbufthick)
+ sslipj=sscalelip(fracinbuf)
+ ssgradlipj=sscagradlip(fracinbuf)/lipbufthick
+ else
+ sslipj=1.0d0
+ ssgradlipj=0.0
+ endif
+ else
+ sslipj=0.0d0
+ ssgradlipj=0.0
+ endif
+ aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0
+ & +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+ bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0
+ & +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+C 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??"
+C print *,sslipi,sslipj,bordlipbot,zi,zj
+ dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
+ xj_safe=xj
+ yj_safe=yj
+ zj_safe=zj
+ subchap=0
+ do xshift=-1,1
+ do yshift=-1,1
+ do zshift=-1,1
+ xj=xj_safe+xshift*boxxsize
+ yj=yj_safe+yshift*boxysize
+ zj=zj_safe+zshift*boxzsize
+ dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
+ if(dist_temp.lt.dist_init) then
+ dist_init=dist_temp
+ xj_temp=xj
+ yj_temp=yj
+ zj_temp=zj
+ subchap=1
+ endif
+ enddo
+ enddo
+ enddo
+ if (subchap.eq.1) then
+ xj=xj_temp-xi
+ yj=yj_temp-yi
+ zj=zj_temp-zi
+ else
+ xj=xj_safe-xi
+ yj=yj_safe-yi
+ zj=zj_safe-zi
+ endif
dxj=dc_norm(1,nres+j)
dyj=dc_norm(2,nres+j)
dzj=dc_norm(3,nres+j)
+C xj=xj-xi
+C yj=yj-yi
+C zj=zj-zi
c write (iout,*) "dcnorj",dxi*dxi+dyi*dyi+dzi*dzi
c write (iout,*) "j",j," dc_norm",
c & dc_norm(1,nres+j),dc_norm(2,nres+j),dc_norm(3,nres+j)
rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
rij=dsqrt(rrij)
+ sss=sscale((1.0d0/rij)/sigma(itypi,itypj))
+ sssgrad=sscagrad((1.0d0/rij)/sigma(itypi,itypj))
+
+c write (iout,'(a7,4f8.3)')
+c & "ssscale",sss,((1.0d0/rij)/sigma(itypi,itypj)),r_cut,rlamb
+ if (sss.gt.0.0d0) then
C Calculate angle-dependent terms of energy and contributions to their
C derivatives.
call sc_angular
c---------------------------------------------------------------
rij_shift=1.0D0/rij_shift
fac=rij_shift**expon
- e1=fac*fac*aa(itypi,itypj)
- e2=fac*bb(itypi,itypj)
+C here to start with
+C if (c(i,3).gt.
+ faclip=fac
+ e1=fac*fac*aa
+ e2=fac*bb
evdwij=eps1*eps2rt*eps3rt*(e1+e2)
eps2der=evdwij*eps3rt
eps3der=evdwij*eps2rt
+C write(63,'(2i3,2e10.3,2f10.5)') i,j,aa,bb, evdwij,
+C &((sslipi+sslipj)/2.0d0+
+C &(2.0d0-sslipi-sslipj)/2.0d0)
c write (iout,*) "sigsq",sigsq," sig",sig," eps2rt",eps2rt,
c & " eps3rt",eps3rt," eps1",eps1," e1",e1," e2",e2
evdwij=evdwij*eps2rt*eps3rt
- evdw=evdw+evdwij
+ evdw=evdw+evdwij*sss
if (lprn) then
- sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
- epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
+ sigm=dabs(aa/bb)**(1.0D0/6.0D0)
+ epsi=bb**2/aa
write (iout,'(2(a3,i3,2x),17(0pf7.3))')
& restyp(itypi),i,restyp(itypj),j,
& epsi,sigm,chi1,chi2,chip1,chip2,
fac=-expon*(e1+evdwij)*rij_shift
sigder=fac*sigder
fac=rij*fac
+c print '(2i4,6f8.4)',i,j,sss,sssgrad*
+c & evdwij,fac,sigma(itypi,itypj),expon
+ fac=fac+evdwij/sss*sssgrad/sigma(itypi,itypj)*rij
c fac=0.0d0
C Calculate the radial part of the gradient
+ gg_lipi(3)=eps1*(eps2rt*eps2rt)
+ &*(eps3rt*eps3rt)*sss/2.0d0*(faclip*faclip*
+ & (aa_lip(itypi,itypj)-aa_aq(itypi,itypj))
+ &+faclip*(bb_lip(itypi,itypj)-bb_aq(itypi,itypj)))
+ gg_lipj(3)=ssgradlipj*gg_lipi(3)
+ gg_lipi(3)=gg_lipi(3)*ssgradlipi
+C gg_lipi(3)=0.0d0
+C gg_lipj(3)=0.0d0
gg(1)=xj*fac
gg(2)=yj*fac
gg(3)=zj*fac
C Calculate angular part of the gradient.
call sc_grad
+ endif
+ ENDIF ! dyn_ss
enddo ! j
enddo ! iint
enddo ! i
+C enddo ! zshift
+C enddo ! yshift
+C enddo ! xshift
c write (iout,*) "Number of loop steps in EGB:",ind
cccc energy_dec=.false.
return
C
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
+ include 'COMMON.CONTROL'
include 'COMMON.GEO'
include 'COMMON.VAR'
include 'COMMON.LOCAL'
include 'COMMON.INTERACT'
include 'COMMON.IOUNITS'
include 'COMMON.CALC'
+ include 'COMMON.SPLITELE'
+ include 'COMMON.SBRIDGE'
+ integer xshift,yshift,zshift
common /srutu/ icall
- logical lprn
+ logical lprn
evdw=0.0D0
c print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon
evdw=0.0D0
c if (icall.eq.0) lprn=.true.
ind=0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- if (itypi.eq.21) cycle
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ if (itypi.eq.ntyp1) cycle
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
+c write (iout,*)"xi yi zi box",xi,yi,zi,boxxsize,boxysize,boxzsize
+ xi=mod(xi,boxxsize)
+ if (xi.lt.0) xi=xi+boxxsize
+ yi=mod(yi,boxysize)
+ if (yi.lt.0) yi=yi+boxysize
+ zi=mod(zi,boxzsize)
+ if (zi.lt.0) zi=zi+boxzsize
+c write (iout,*)"xi yi zi box",xi,yi,zi,boxxsize,boxysize,boxzsize
+C define scaling factor for lipids
+
+C if (positi.le.0) positi=positi+boxzsize
+C print *,i
+C first for peptide groups
+c for each residue check if it is in lipid or lipid water border area
+ if ((zi.gt.bordlipbot)
+ & .and.(zi.lt.bordliptop)) then
+C the energy transfer exist
+ if (zi.lt.buflipbot) then
+C what fraction I am in
+ fracinbuf=1.0d0-
+ & ((zi-bordlipbot)/lipbufthick)
+C lipbufthick is thickenes of lipid buffore
+ sslipi=sscalelip(fracinbuf)
+ ssgradlipi=-sscagradlip(fracinbuf)/lipbufthick
+ elseif (zi.gt.bufliptop) then
+ fracinbuf=1.0d0-((bordliptop-zi)/lipbufthick)
+ sslipi=sscalelip(fracinbuf)
+ ssgradlipi=sscagradlip(fracinbuf)/lipbufthick
+ else
+ sslipi=1.0d0
+ ssgradlipi=0.0
+ endif
+ else
+ sslipi=0.0d0
+ ssgradlipi=0.0
+ endif
+
dxi=dc_norm(1,nres+i)
dyi=dc_norm(2,nres+i)
dzi=dc_norm(3,nres+i)
C
do iint=1,nint_gr(i)
do j=istart(i,iint),iend(i,iint)
+ IF (dyn_ss_mask(i).and.dyn_ss_mask(j)) THEN
+
+ call dyn_ssbond_ene(i,j,evdwij)
+ evdw=evdw+evdwij
+ if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a3)')
+ & 'evdw',i,j,evdwij,' ss'
+C triple bond artifac removal
+ do k=j+1,iend(i,iint)
+C search over all next residues
+ if (dyn_ss_mask(k)) then
+C check if they are cysteins
+C write(iout,*) 'k=',k
+
+c write(iout,*) "PRZED TRI", evdwij
+ evdwij_przed_tri=evdwij
+ call triple_ssbond_ene(i,j,k,evdwij)
+c if(evdwij_przed_tri.ne.evdwij) then
+c write (iout,*) "TRI:", evdwij, evdwij_przed_tri
+c endif
+
+c write(iout,*) "PO TRI", evdwij
+C call the energy function that removes the artifical triple disulfide
+C bond the soubroutine is located in ssMD.F
+ evdw=evdw+evdwij
+ if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a3)')
+ & 'evdw',i,j,evdwij,'tss'
+ endif!dyn_ss_mask(k)
+ enddo! k
+ ELSE
ind=ind+1
- itypj=itype(j)
- if (itypj.eq.21) cycle
+ itypj=iabs(itype(j))
+ if (itypj.eq.ntyp1) cycle
c dscj_inv=dsc_inv(itypj)
dscj_inv=vbld_inv(j+nres)
sig0ij=sigma(itypi,itypj)
c alf1=0.0D0
c alf2=0.0D0
c alf12=0.0D0
- xj=c(1,nres+j)-xi
- yj=c(2,nres+j)-yi
- zj=c(3,nres+j)-zi
+C xj=c(1,nres+j)-xi
+C yj=c(2,nres+j)-yi
+C zj=c(3,nres+j)-zi
+ xj=c(1,nres+j)
+ yj=c(2,nres+j)
+ zj=c(3,nres+j)
+c write (iout,*)"xj yj zj box",xj,yj,zj,boxxsize,boxysize,boxzsize
+ xj=mod(xj,boxxsize)
+ if (xj.lt.0) xj=xj+boxxsize
+ yj=mod(yj,boxysize)
+ if (yj.lt.0) yj=yj+boxysize
+ zj=mod(zj,boxzsize)
+ if (zj.lt.0) zj=zj+boxzsize
+c write (iout,*)"xj yj zj box",xj,yj,zj,boxxsize,boxysize,boxzsize
+ if ((zj.gt.bordlipbot)
+ & .and.(zj.lt.bordliptop)) then
+C the energy transfer exist
+ if (zj.lt.buflipbot) then
+C what fraction I am in
+ fracinbuf=1.0d0-
+ & ((zj-bordlipbot)/lipbufthick)
+C lipbufthick is thickenes of lipid buffore
+ sslipj=sscalelip(fracinbuf)
+ ssgradlipj=-sscagradlip(fracinbuf)/lipbufthick
+ elseif (zj.gt.bufliptop) then
+ fracinbuf=1.0d0-((bordliptop-zj)/lipbufthick)
+ sslipj=sscalelip(fracinbuf)
+ ssgradlipj=sscagradlip(fracinbuf)/lipbufthick
+ else
+ sslipj=1.0d0
+ ssgradlipj=0.0
+ endif
+ else
+ sslipj=0.0d0
+ ssgradlipj=0.0
+ endif
+ aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0
+ & +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+ bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0
+ & +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+ dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
+c write (iout,*) "dist_init",dist_init
+ xj_safe=xj
+ yj_safe=yj
+ zj_safe=zj
+ subchap=0
+ do xshift=-1,1
+ do yshift=-1,1
+ do zshift=-1,1
+ xj=xj_safe+xshift*boxxsize
+ yj=yj_safe+yshift*boxysize
+ zj=zj_safe+zshift*boxzsize
+ dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
+ if(dist_temp.lt.dist_init) then
+ dist_init=dist_temp
+ xj_temp=xj
+ yj_temp=yj
+ zj_temp=zj
+ subchap=1
+ endif
+ enddo
+ enddo
+ enddo
+ if (subchap.eq.1) then
+ xj=xj_temp-xi
+ yj=yj_temp-yi
+ zj=zj_temp-zi
+ else
+ xj=xj_safe-xi
+ yj=yj_safe-yi
+ zj=zj_safe-zi
+ endif
dxj=dc_norm(1,nres+j)
dyj=dc_norm(2,nres+j)
dzj=dc_norm(3,nres+j)
rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
rij=dsqrt(rrij)
+ sss=sscale((1.0d0/rij)/sigma(itypi,itypj))
+ sssgrad=sscagrad((1.0d0/rij)/sigma(itypi,itypj))
+
+ if (sss.gt.0.0d0) then
+
C Calculate angle-dependent terms of energy and contributions to their
C derivatives.
call sc_angular
c---------------------------------------------------------------
rij_shift=1.0D0/rij_shift
fac=rij_shift**expon
- e1=fac*fac*aa(itypi,itypj)
- e2=fac*bb(itypi,itypj)
+ e1=fac*fac*aa
+ e2=fac*bb
evdwij=eps1*eps2rt*eps3rt*(e1+e2)
eps2der=evdwij*eps3rt
eps3der=evdwij*eps2rt
e_augm=augm(itypi,itypj)*fac_augm
evdwij=evdwij*eps2rt*eps3rt
evdw=evdw+evdwij+e_augm
+ if (energy_dec) write (iout,'(a6,2i5,0pf7.3)')
+ & 'evdw',i,j,evdwij
if (lprn) then
- sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
- epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
+ sigm=dabs(aa/bb)**(1.0D0/6.0D0)
+ epsi=bb**2/aa
write (iout,'(2(a3,i3,2x),17(0pf7.3))')
& restyp(itypi),i,restyp(itypj),j,
& epsi,sigm,sig,(augm(itypi,itypj)/epsi)**(1.0D0/12.0D0),
fac=-expon*(e1+evdwij)*rij_shift
sigder=fac*sigder
fac=rij*fac-2*expon*rrij*e_augm
+ fac=fac+evdwij/sss*sssgrad/sigma(itypi,itypj)*rij
C Calculate the radial part of the gradient
gg(1)=xj*fac
gg(2)=yj*fac
gg(3)=zj*fac
+c write (iout,*) "sss",sss," fac",fac," gg",gg
C Calculate angular part of the gradient.
call sc_grad
+ endif
+ ENDIF
enddo ! j
enddo ! iint
enddo ! i
include 'COMMON.CALC'
include 'COMMON.IOUNITS'
double precision dcosom1(3),dcosom2(3)
+cc print *,'sss=',sss
eom1=eps2der*eps2rt_om1-2.0D0*alf1*eps3der+sigder*sigsq_om1
eom2=eps2der*eps2rt_om2+2.0D0*alf2*eps3der+sigder*sigsq_om2
eom12=evdwij*eps1_om12+eps2der*eps2rt_om12
dcosom2(k)=rij*(dc_norm(k,nres+j)-om2*erij(k))
enddo
do k=1,3
- gg(k)=gg(k)+eom1*dcosom1(k)+eom2*dcosom2(k)
+ gg(k)=(gg(k)+eom1*dcosom1(k)+eom2*dcosom2(k))*sss
enddo
c write (iout,*) "gg",(gg(k),k=1,3)
do k=1,3
- gvdwx(k,i)=gvdwx(k,i)-gg(k)
+ gvdwx(k,i)=gvdwx(k,i)-gg(k)+gg_lipi(k)
& +(eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i))
- & +eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv
- gvdwx(k,j)=gvdwx(k,j)+gg(k)
+ & +eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv*sss
+ gvdwx(k,j)=gvdwx(k,j)+gg(k)+gg_lipj(k)
& +(eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,nres+j))
- & +eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv
+ & +eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv*sss
c write (iout,*)(eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i))
c & +eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv
c write (iout,*)(eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,nres+j))
cgrad enddo
cgrad enddo
do l=1,3
- gvdwc(l,i)=gvdwc(l,i)-gg(l)
- gvdwc(l,j)=gvdwc(l,j)+gg(l)
+ gvdwc(l,i)=gvdwc(l,i)-gg(l)+gg_lipi(l)
+ gvdwc(l,j)=gvdwc(l,j)+gg(l)+gg_lipj(l)
enddo
return
end
cd print *,'Entering Esoft_sphere nnt=',nnt,' nct=',nct
evdw=0.0D0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- if (itypi.eq.21) cycle
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ if (itypi.eq.ntyp1) cycle
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
cd write (iout,*) 'i=',i,' iint=',iint,' istart=',istart(i,iint),
cd & 'iend=',iend(i,iint)
do j=istart(i,iint),iend(i,iint)
- itypj=itype(j)
- if (itypj.eq.21) cycle
+ itypj=iabs(itype(j))
+ if (itypj.eq.ntyp1) cycle
xj=c(1,nres+j)-xi
yj=c(2,nres+j)-yi
zj=c(3,nres+j)-zi
include 'COMMON.VECTORS'
include 'COMMON.FFIELD'
dimension ggg(3)
-cd write(iout,*) 'In EELEC_soft_sphere'
+ integer xshift,yshift,zshift
+C write(iout,*) 'In EELEC_soft_sphere'
ees=0.0D0
evdw1=0.0D0
eel_loc=0.0d0
eello_turn4=0.0d0
ind=0
do i=iatel_s,iatel_e
- if (itype(i).eq.21 .or. itype(i+1).eq.21) cycle
+ if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle
dxi=dc(1,i)
dyi=dc(2,i)
dzi=dc(3,i)
xmedi=c(1,i)+0.5d0*dxi
ymedi=c(2,i)+0.5d0*dyi
zmedi=c(3,i)+0.5d0*dzi
+ xmedi=mod(xmedi,boxxsize)
+ if (xmedi.lt.0) xmedi=xmedi+boxxsize
+ ymedi=mod(ymedi,boxysize)
+ if (ymedi.lt.0) ymedi=ymedi+boxysize
+ zmedi=mod(zmedi,boxzsize)
+ if (zmedi.lt.0) zmedi=zmedi+boxzsize
num_conti=0
c write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i)
do j=ielstart(i),ielend(i)
- if (itype(j).eq.21 .or. itype(j+1).eq.21) cycle
+ if (itype(j).eq.ntyp1 .or. itype(j+1).eq.ntyp1) cycle
ind=ind+1
iteli=itel(i)
itelj=itel(j)
dxj=dc(1,j)
dyj=dc(2,j)
dzj=dc(3,j)
- xj=c(1,j)+0.5D0*dxj-xmedi
- yj=c(2,j)+0.5D0*dyj-ymedi
- zj=c(3,j)+0.5D0*dzj-zmedi
+ xj=c(1,j)+0.5D0*dxj
+ yj=c(2,j)+0.5D0*dyj
+ zj=c(3,j)+0.5D0*dzj
+ xj=mod(xj,boxxsize)
+ if (xj.lt.0) xj=xj+boxxsize
+ yj=mod(yj,boxysize)
+ if (yj.lt.0) yj=yj+boxysize
+ zj=mod(zj,boxzsize)
+ if (zj.lt.0) zj=zj+boxzsize
+ dist_init=(xj-xmedi)**2+(yj-ymedi)**2+(zj-zmedi)**2
+ xj_safe=xj
+ yj_safe=yj
+ zj_safe=zj
+ isubchap=0
+ do xshift=-1,1
+ do yshift=-1,1
+ do zshift=-1,1
+ xj=xj_safe+xshift*boxxsize
+ yj=yj_safe+yshift*boxysize
+ zj=zj_safe+zshift*boxzsize
+ dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
+ if(dist_temp.lt.dist_init) then
+ dist_init=dist_temp
+ xj_temp=xj
+ yj_temp=yj
+ zj_temp=zj
+ isubchap=1
+ endif
+ enddo
+ enddo
+ enddo
+ if (isubchap.eq.1) then
+ xj=xj_temp-xmedi
+ yj=yj_temp-ymedi
+ zj=zj_temp-zmedi
+ else
+ xj=xj_safe-xmedi
+ yj=yj_safe-ymedi
+ zj=zj_safe-zmedi
+ endif
rij=xj*xj+yj*yj+zj*zj
+ sss=sscale(sqrt(rij))
+ sssgrad=sscagrad(sqrt(rij))
if (rij.lt.r0ijsq) then
evdw1ij=0.25d0*(rij-r0ijsq)**2
fac=rij-r0ijsq
evdw1ij=0.0d0
fac=0.0d0
endif
- evdw1=evdw1+evdw1ij
+ evdw1=evdw1+evdw1ij*sss
C
C Calculate contributions to the Cartesian gradient.
C
- ggg(1)=fac*xj
- ggg(2)=fac*yj
- ggg(3)=fac*zj
+ ggg(1)=fac*xj*sssgrad
+ ggg(2)=fac*yj*sssgrad
+ ggg(3)=fac*zj*sssgrad
do k=1,3
gvdwpp(k,i)=gvdwpp(k,i)-ggg(k)
gvdwpp(k,j)=gvdwpp(k,j)+ggg(k)
& ivec_displ(0),MPI_UYZGRAD,FG_COMM1,IERR)
time_gather=time_gather+MPI_Wtime()-time00
endif
-c if (fg_rank.eq.0) then
-c write (iout,*) "Arrays UY and UZ"
-c do i=1,nres-1
-c write (iout,'(i5,3f10.5,5x,3f10.5)') i,(uy(k,i),k=1,3),
-c & (uz(k,i),k=1,3)
-c enddo
-c endif
+#endif
+#ifdef DEBUG
+ if (fg_rank.eq.0) then
+ write (iout,*) "Arrays UY and UZ"
+ do i=1,nres-1
+ write (iout,'(i5,3f10.5,5x,3f10.5)') i,(uy(k,i),k=1,3),
+ & (uz(k,i),k=1,3)
+ enddo
+ endif
#endif
return
end
C Compute the virtual-bond-torsional-angle dependent quantities needed
C to calculate the el-loc multibody terms of various order.
C
+c write(iout,*) 'nphi=',nphi,nres
+c write(iout,*) "itype2loc",itype2loc
+#ifdef PARMAT
+ do i=ivec_start+2,ivec_end+2
+#else
+ do i=3,nres+1
+#endif
+ 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
+c write(iout,*),i
+#ifdef NEWCORR
+ cost1=dcos(theta(i-1))
+ sint1=dsin(theta(i-1))
+ sint1sq=sint1*sint1
+ sint1cub=sint1sq*sint1
+ sint1cost1=2*sint1*cost1
+c write (iout,*) "bnew1",i,iti
+c write (iout,*) (bnew1(k,1,iti),k=1,3)
+c write (iout,*) (bnew1(k,2,iti),k=1,3)
+c write (iout,*) "bnew2",i,iti
+c write (iout,*) (bnew2(k,1,iti),k=1,3)
+c write (iout,*) (bnew2(k,2,iti),k=1,3)
+ do k=1,2
+ b1k=bnew1(1,k,iti)+(bnew1(2,k,iti)+bnew1(3,k,iti)*cost1)*cost1
+ b1(k,i-2)=sint1*b1k
+ gtb1(k,i-2)=cost1*b1k-sint1sq*
+ & (bnew1(2,k,iti)+2*bnew1(3,k,iti)*cost1)
+ b2k=bnew2(1,k,iti)+(bnew2(2,k,iti)+bnew2(3,k,iti)*cost1)*cost1
+ b2(k,i-2)=sint1*b2k
+ gtb2(k,i-2)=cost1*b2k-sint1sq*
+ & (bnew2(2,k,iti)+2*bnew2(3,k,iti)*cost1)
+ enddo
+ do k=1,2
+ aux=ccnew(1,k,iti)+(ccnew(2,k,iti)+ccnew(3,k,iti)*cost1)*cost1
+ cc(1,k,i-2)=sint1sq*aux
+ gtcc(1,k,i-2)=sint1cost1*aux-sint1cub*
+ & (ccnew(2,k,iti)+2*ccnew(3,k,iti)*cost1)
+ aux=ddnew(1,k,iti)+(ddnew(2,k,iti)+ddnew(3,k,iti)*cost1)*cost1
+ dd(1,k,i-2)=sint1sq*aux
+ gtdd(1,k,i-2)=sint1cost1*aux-sint1cub*
+ & (ddnew(2,k,iti)+2*ddnew(3,k,iti)*cost1)
+ enddo
+ cc(2,1,i-2)=cc(1,2,i-2)
+ cc(2,2,i-2)=-cc(1,1,i-2)
+ gtcc(2,1,i-2)=gtcc(1,2,i-2)
+ gtcc(2,2,i-2)=-gtcc(1,1,i-2)
+ dd(2,1,i-2)=dd(1,2,i-2)
+ dd(2,2,i-2)=-dd(1,1,i-2)
+ gtdd(2,1,i-2)=gtdd(1,2,i-2)
+ gtdd(2,2,i-2)=-gtdd(1,1,i-2)
+ do k=1,2
+ do l=1,2
+ aux=eenew(1,l,k,iti)+eenew(2,l,k,iti)*cost1
+ EE(l,k,i-2)=sint1sq*aux
+ gtEE(l,k,i-2)=sint1cost1*aux-sint1cub*eenew(2,l,k,iti)
+ enddo
+ enddo
+ EE(1,1,i-2)=EE(1,1,i-2)+e0new(1,iti)*cost1
+ EE(1,2,i-2)=EE(1,2,i-2)+e0new(2,iti)+e0new(3,iti)*cost1
+ EE(2,1,i-2)=EE(2,1,i-2)+e0new(2,iti)*cost1+e0new(3,iti)
+ EE(2,2,i-2)=EE(2,2,i-2)-e0new(1,iti)
+ gtEE(1,1,i-2)=gtEE(1,1,i-2)-e0new(1,iti)*sint1
+ gtEE(1,2,i-2)=gtEE(1,2,i-2)-e0new(3,iti)*sint1
+ gtEE(2,1,i-2)=gtEE(2,1,i-2)-e0new(2,iti)*sint1
+c b1tilde(1,i-2)=b1(1,i-2)
+c b1tilde(2,i-2)=-b1(2,i-2)
+c b2tilde(1,i-2)=b2(1,i-2)
+c b2tilde(2,i-2)=-b2(2,i-2)
+#ifdef DEBUG
+ write (iout,*) 'i=',i-2,gtb1(2,i-2),gtb1(1,i-2)
+ write(iout,*) 'b1=',(b1(k,i-2),k=1,2)
+ write(iout,*) 'b2=',(b2(k,i-2),k=1,2)
+ write (iout,*) 'theta=', theta(i-1)
+#endif
+#else
+ if (i.gt. nnt+2 .and. i.lt.nct+2) then
+ iti = itype2loc(itype(i-2))
+ else
+ iti=nloctyp
+ endif
+c write (iout,*) "i",i-1," itype",itype(i-2)," iti",iti
+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)
+ b2(2,i-2)=b(4,iti)
+ do k=1,2
+ do l=1,2
+ CC(k,l,i-2)=ccold(k,l,iti)
+ DD(k,l,i-2)=ddold(k,l,iti)
+ EE(k,l,i-2)=eeold(k,l,iti)
+ enddo
+ enddo
+#endif
+ b1tilde(1,i-2)= b1(1,i-2)
+ b1tilde(2,i-2)=-b1(2,i-2)
+ b2tilde(1,i-2)= b2(1,i-2)
+ b2tilde(2,i-2)=-b2(2,i-2)
+c
+ Ctilde(1,1,i-2)= CC(1,1,i-2)
+ Ctilde(1,2,i-2)= CC(1,2,i-2)
+ Ctilde(2,1,i-2)=-CC(2,1,i-2)
+ Ctilde(2,2,i-2)=-CC(2,2,i-2)
+c
+ Dtilde(1,1,i-2)= DD(1,1,i-2)
+ Dtilde(1,2,i-2)= DD(1,2,i-2)
+ Dtilde(2,1,i-2)=-DD(2,1,i-2)
+ Dtilde(2,2,i-2)=-DD(2,2,i-2)
+#ifdef DEBUG
+ write(iout,*) "i",i," iti",iti
+ write(iout,*) 'b1=',(b1(k,i-2),k=1,2)
+ write(iout,*) 'b2=',(b2(k,i-2),k=1,2)
+#endif
+ enddo
#ifdef PARMAT
do i=ivec_start+2,ivec_end+2
#else
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+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
cd write (iout,*) '*******i',i,' iti1',iti
cd write (iout,*) 'b1',b1(:,iti)
cd write (iout,*) 'Ug',Ug(:,:,i-2)
c if (i .gt. iatel_s+2) then
if (i .gt. nnt+2) then
- call matvec2(Ug(1,1,i-2),b2(1,iti),Ub2(1,i-2))
- call matmat2(EE(1,1,iti),Ug(1,1,i-2),EUg(1,1,i-2))
+ call matvec2(Ug(1,1,i-2),b2(1,i-2),Ub2(1,i-2))
+#ifdef NEWCORR
+ call matvec2(Ug(1,1,i-2),gtb2(1,i-2),gUb2(1,i-2))
+c write (iout,*) Ug(1,1,i-2),gtb2(1,i-2),gUb2(1,i-2),"chuj"
+#endif
+c write(iout,*) "co jest kurwa", iti, EE(1,1,i),EE(2,1,i),
+c & EE(1,2,iti),EE(2,2,i)
+ call matmat2(EE(1,1,i-2),Ug(1,1,i-2),EUg(1,1,i-2))
+ call matmat2(gtEE(1,1,i-2),Ug(1,1,i-2),gtEUg(1,1,i-2))
+c write(iout,*) "Macierz EUG",
+c & eug(1,1,i-2),eug(1,2,i-2),eug(2,1,i-2),
+c & eug(2,2,i-2)
if (wcorr4.gt.0.0d0 .or. wcorr5.gt.0.0d0 .or. wcorr6.gt.0.0d0)
& then
- call matmat2(CC(1,1,iti),Ug(1,1,i-2),CUg(1,1,i-2))
- call matmat2(DD(1,1,iti),Ug(1,1,i-2),DUg(1,1,i-2))
- call matmat2(Dtilde(1,1,iti),Ug2(1,1,i-2),DtUg2(1,1,i-2))
- call matvec2(Ctilde(1,1,iti1),obrot(1,i-2),Ctobr(1,i-2))
- call matvec2(Dtilde(1,1,iti),obrot2(1,i-2),Dtobr2(1,i-2))
+ call matmat2(CC(1,1,i-2),Ug(1,1,i-2),CUg(1,1,i-2))
+ call matmat2(DD(1,1,i-2),Ug(1,1,i-2),DUg(1,1,i-2))
+ call matmat2(Dtilde(1,1,i-2),Ug2(1,1,i-2),DtUg2(1,1,i-2))
+ call matvec2(Ctilde(1,1,i-1),obrot(1,i-2),Ctobr(1,i-2))
+ call matvec2(Dtilde(1,1,i-2),obrot2(1,i-2),Dtobr2(1,i-2))
endif
else
do k=1,2
enddo
enddo
endif
- call matvec2(Ugder(1,1,i-2),b2(1,iti),Ub2der(1,i-2))
- call matmat2(EE(1,1,iti),Ugder(1,1,i-2),EUgder(1,1,i-2))
+ call matvec2(Ugder(1,1,i-2),b2(1,i-2),Ub2der(1,i-2))
+ call matmat2(EE(1,1,i-2),Ugder(1,1,i-2),EUgder(1,1,i-2))
do k=1,2
muder(k,i-2)=Ub2der(k,i-2)
enddo
c if (i.gt. iatel_s+1 .and. i.lt.iatel_e+4) then
if (i.gt. nnt+1 .and. i.lt.nct+1) then
- iti1 = itortyp(itype(i-1))
+ if (itype(i-1).le.ntyp) then
+ iti1 = itype2loc(itype(i-1))
+ else
+ iti1=nloctyp
+ endif
else
- iti1=ntortyp+1
+ iti1=nloctyp
endif
do k=1,2
- mu(k,i-2)=Ub2(k,i-2)+b1(k,iti1)
+ mu(k,i-2)=Ub2(k,i-2)+b1(k,i-1)
+c mu(k,i-2)=b1(k,i-1)
+c mu(k,i-2)=Ub2(k,i-2)
enddo
-cd write (iout,*) 'mu ',mu(:,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)
+#endif
cd write (iout,*) 'mu1',mu1(:,i-2)
cd write (iout,*) 'mu2',mu2(:,i-2)
+cd write (iout,*) 'mu',i-2,mu(:,i-2)
if (wcorr4.gt.0.0d0 .or. wcorr5.gt.0.0d0 .or.wcorr6.gt.0.0d0)
& then
- call matmat2(CC(1,1,iti1),Ugder(1,1,i-2),CUgder(1,1,i-2))
- call matmat2(DD(1,1,iti),Ugder(1,1,i-2),DUgder(1,1,i-2))
- call matmat2(Dtilde(1,1,iti),Ug2der(1,1,i-2),DtUg2der(1,1,i-2))
- call matvec2(Ctilde(1,1,iti1),obrot_der(1,i-2),Ctobrder(1,i-2))
- call matvec2(Dtilde(1,1,iti),obrot2_der(1,i-2),Dtobr2der(1,i-2))
+ call matmat2(CC(1,1,i-1),Ugder(1,1,i-2),CUgder(1,1,i-2))
+ call matmat2(DD(1,1,i-2),Ugder(1,1,i-2),DUgder(1,1,i-2))
+ call matmat2(Dtilde(1,1,i-2),Ug2der(1,1,i-2),DtUg2der(1,1,i-2))
+ call matvec2(Ctilde(1,1,i-1),obrot_der(1,i-2),Ctobrder(1,i-2))
+ call matvec2(Dtilde(1,1,i-2),obrot2_der(1,i-2),Dtobr2der(1,i-2))
C Vectors and matrices dependent on a single virtual-bond dihedral.
- call matvec2(DD(1,1,iti),b1tilde(1,iti1),auxvec(1))
+ call matvec2(DD(1,1,i-2),b1tilde(1,i-1),auxvec(1))
call matvec2(Ug2(1,1,i-2),auxvec(1),Ug2Db1t(1,i-2))
call matvec2(Ug2der(1,1,i-2),auxvec(1),Ug2Db1tder(1,i-2))
- call matvec2(CC(1,1,iti1),Ub2(1,i-2),CUgb2(1,i-2))
- call matvec2(CC(1,1,iti1),Ub2der(1,i-2),CUgb2der(1,i-2))
- call matmat2(EUg(1,1,i-2),CC(1,1,iti1),EUgC(1,1,i-2))
- call matmat2(EUgder(1,1,i-2),CC(1,1,iti1),EUgCder(1,1,i-2))
- call matmat2(EUg(1,1,i-2),DD(1,1,iti1),EUgD(1,1,i-2))
- call matmat2(EUgder(1,1,i-2),DD(1,1,iti1),EUgDder(1,1,i-2))
+ call matvec2(CC(1,1,i-1),Ub2(1,i-2),CUgb2(1,i-2))
+ call matvec2(CC(1,1,i-1),Ub2der(1,i-2),CUgb2der(1,i-2))
+ call matmat2(EUg(1,1,i-2),CC(1,1,i-1),EUgC(1,1,i-2))
+ call matmat2(EUgder(1,1,i-2),CC(1,1,i-1),EUgCder(1,1,i-2))
+ call matmat2(EUg(1,1,i-2),DD(1,1,i-1),EUgD(1,1,i-2))
+ call matmat2(EUgder(1,1,i-2),DD(1,1,i-1),EUgDder(1,1,i-2))
endif
enddo
C Matrices dependent on two consecutive virtual-bond dihedrals.
#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
include 'COMMON.VECTORS'
include 'COMMON.FFIELD'
include 'COMMON.TIME1'
+ include 'COMMON.SPLITELE'
dimension ggg(3),gggp(3),gggm(3),erij(3),dcosb(3),dcosg(3),
& erder(3,3),uryg(3,3),urzg(3,3),vryg(3,3),vrzg(3,3)
double precision acipa(2,2),agg(3,4),aggi(3,4),aggi1(3,4),
- & aggj(3,4),aggj1(3,4),a_temp(2,2),muij(4)
+ & aggj(3,4),aggj1(3,4),a_temp(2,2),muij(4),gmuij(4)
common /locel/ a_temp,agg,aggi,aggi1,aggj,aggj1,a22,a23,a32,a33,
& dxi,dyi,dzi,dx_normi,dy_normi,dz_normi,xmedi,ymedi,zmedi,
& num_conti,j1,j2
C
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 (itype(i).eq.21 .or. itype(i+1).eq.21
- & .or. itype(i+2).eq.21 .or. itype(i+3).eq.21) 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
+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
+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)
xmedi=c(1,i)+0.5d0*dxi
ymedi=c(2,i)+0.5d0*dyi
zmedi=c(3,i)+0.5d0*dzi
+ xmedi=mod(xmedi,boxxsize)
+ if (xmedi.lt.0) xmedi=xmedi+boxxsize
+ ymedi=mod(ymedi,boxysize)
+ if (ymedi.lt.0) ymedi=ymedi+boxysize
+ zmedi=mod(zmedi,boxzsize)
+ if (zmedi.lt.0) zmedi=zmedi+boxzsize
num_conti=0
call eelecij(i,i+2,ees,evdw1,eel_loc)
if (wturn3.gt.0.0d0) call eturn3(i,eello_turn3)
num_cont_hb(i)=num_conti
enddo
do i=iturn4_start,iturn4_end
- if (itype(i).eq.21 .or. itype(i+1).eq.21
- & .or. itype(i+3).eq.21
- & .or. itype(i+4).eq.21) 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
+c & .or.((i+5).gt.nres)
+c & .or.((i-1).le.0)
+C end of changes suggested by Ana
+ & .or. itype(i+3).eq.ntyp1
+ & .or. itype(i+4).eq.ntyp1
+c & .or. itype(i+5).eq.ntyp1
+c & .or. itype(i).eq.ntyp1
+c & .or. itype(i-1).eq.ntyp1
+ & ) cycle
dxi=dc(1,i)
dyi=dc(2,i)
dzi=dc(3,i)
xmedi=c(1,i)+0.5d0*dxi
ymedi=c(2,i)+0.5d0*dyi
zmedi=c(3,i)+0.5d0*dzi
+C Return atom into box, boxxsize is size of box in x dimension
+c 194 continue
+c if (xmedi.gt.((0.5d0)*boxxsize)) xmedi=xmedi-boxxsize
+c if (xmedi.lt.((-0.5d0)*boxxsize)) xmedi=xmedi+boxxsize
+C Condition for being inside the proper box
+c if ((xmedi.gt.((0.5d0)*boxxsize)).or.
+c & (xmedi.lt.((-0.5d0)*boxxsize))) then
+c go to 194
+c endif
+c 195 continue
+c if (ymedi.gt.((0.5d0)*boxysize)) ymedi=ymedi-boxysize
+c if (ymedi.lt.((-0.5d0)*boxysize)) ymedi=ymedi+boxysize
+C Condition for being inside the proper box
+c if ((ymedi.gt.((0.5d0)*boxysize)).or.
+c & (ymedi.lt.((-0.5d0)*boxysize))) then
+c go to 195
+c endif
+c 196 continue
+c if (zmedi.gt.((0.5d0)*boxzsize)) zmedi=zmedi-boxzsize
+c if (zmedi.lt.((-0.5d0)*boxzsize)) zmedi=zmedi+boxzsize
+C Condition for being inside the proper box
+c if ((zmedi.gt.((0.5d0)*boxzsize)).or.
+c & (zmedi.lt.((-0.5d0)*boxzsize))) then
+c go to 196
+c endif
+ xmedi=mod(xmedi,boxxsize)
+ if (xmedi.lt.0) xmedi=xmedi+boxxsize
+ ymedi=mod(ymedi,boxysize)
+ if (ymedi.lt.0) ymedi=ymedi+boxysize
+ zmedi=mod(zmedi,boxzsize)
+ if (zmedi.lt.0) zmedi=zmedi+boxzsize
+
num_conti=num_cont_hb(i)
+c write(iout,*) "JESTEM W PETLI"
call eelecij(i,i+3,ees,evdw1,eel_loc)
- if (wturn4.gt.0.0d0 .and. itype(i+2).ne.21)
+ if (wturn4.gt.0.0d0 .and. itype(i+2).ne.ntyp1)
& call eturn4(i,eello_turn4)
num_cont_hb(i)=num_conti
enddo ! i
+C Loop over all neighbouring boxes
+C do xshift=-1,1
+C do yshift=-1,1
+C do zshift=-1,1
c
c Loop over all pairs of interacting peptide groups except i,i+2 and i,i+3
c
+CTU KURWA
do i=iatel_s,iatel_e
- if (itype(i).eq.21 .or. itype(i+1).eq.21) 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
+c & .or.((i+2).gt.nres)
+c & .or.((i-1).le.0)
+C end of changes by Ana
+c & .or. itype(i+2).eq.ntyp1
+c & .or. itype(i-1).eq.ntyp1
+ & ) cycle
dxi=dc(1,i)
dyi=dc(2,i)
dzi=dc(3,i)
xmedi=c(1,i)+0.5d0*dxi
ymedi=c(2,i)+0.5d0*dyi
zmedi=c(3,i)+0.5d0*dzi
+ xmedi=mod(xmedi,boxxsize)
+ if (xmedi.lt.0) xmedi=xmedi+boxxsize
+ ymedi=mod(ymedi,boxysize)
+ if (ymedi.lt.0) ymedi=ymedi+boxysize
+ zmedi=mod(zmedi,boxzsize)
+ if (zmedi.lt.0) zmedi=zmedi+boxzsize
+C xmedi=xmedi+xshift*boxxsize
+C ymedi=ymedi+yshift*boxysize
+C zmedi=zmedi+zshift*boxzsize
+
+C Return tom into box, boxxsize is size of box in x dimension
+c 164 continue
+c if (xmedi.gt.((xshift+0.5d0)*boxxsize)) xmedi=xmedi-boxxsize
+c if (xmedi.lt.((xshift-0.5d0)*boxxsize)) xmedi=xmedi+boxxsize
+C Condition for being inside the proper box
+c if ((xmedi.gt.((xshift+0.5d0)*boxxsize)).or.
+c & (xmedi.lt.((xshift-0.5d0)*boxxsize))) then
+c go to 164
+c endif
+c 165 continue
+c if (ymedi.gt.((yshift+0.5d0)*boxysize)) ymedi=ymedi-boxysize
+c if (ymedi.lt.((yshift-0.5d0)*boxysize)) ymedi=ymedi+boxysize
+C Condition for being inside the proper box
+c if ((ymedi.gt.((yshift+0.5d0)*boxysize)).or.
+c & (ymedi.lt.((yshift-0.5d0)*boxysize))) then
+c go to 165
+c endif
+c 166 continue
+c if (zmedi.gt.((zshift+0.5d0)*boxzsize)) zmedi=zmedi-boxzsize
+c if (zmedi.lt.((zshift-0.5d0)*boxzsize)) zmedi=zmedi+boxzsize
+cC Condition for being inside the proper box
+c if ((zmedi.gt.((zshift+0.5d0)*boxzsize)).or.
+c & (zmedi.lt.((zshift-0.5d0)*boxzsize))) then
+c go to 166
+c endif
+
c write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i)
num_conti=num_cont_hb(i)
+C I TU KURWA
do j=ielstart(i),ielend(i)
-c write (iout,*) i,j,itype(i),itype(j)
- if (itype(j).eq.21 .or. itype(j+1).eq.21) cycle
+C do j=16,17
+C write (iout,*) i,j
+C if (j.le.1) cycle
+ if (itype(j).eq.ntyp1.or. itype(j+1).eq.ntyp1
+C changes suggested by Ana to avoid out of bounds
+c & .or.((j+2).gt.nres)
+c & .or.((j-1).le.0)
+C end of changes by Ana
+c & .or.itype(j+2).eq.ntyp1
+c & .or.itype(j-1).eq.ntyp1
+ &) cycle
call eelecij(i,j,ees,evdw1,eel_loc)
enddo ! j
num_cont_hb(i)=num_conti
enddo ! i
+C enddo ! zshift
+C enddo ! yshift
+C enddo ! xshift
+
c write (iout,*) "Number of loop steps in EELEC:",ind
cd do i=1,nres
cd write (iout,'(i3,3f10.5,5x,3f10.5)')
include 'COMMON.VECTORS'
include 'COMMON.FFIELD'
include 'COMMON.TIME1'
+ include 'COMMON.SPLITELE'
+ include 'COMMON.SHIELD'
dimension ggg(3),gggp(3),gggm(3),erij(3),dcosb(3),dcosg(3),
& erder(3,3),uryg(3,3),urzg(3,3),vryg(3,3),vrzg(3,3)
double precision acipa(2,2),agg(3,4),aggi(3,4),aggi1(3,4),
- & aggj(3,4),aggj1(3,4),a_temp(2,2),muij(4)
+ & aggj(3,4),aggj1(3,4),a_temp(2,2),muij(4),gmuij1(4),gmuji1(4),
+ & gmuij2(4),gmuji2(4)
common /locel/ a_temp,agg,aggi,aggi1,aggj,aggj1,a22,a23,a32,a33,
& dxi,dyi,dzi,dx_normi,dy_normi,dz_normi,xmedi,ymedi,zmedi,
& num_conti,j1,j2
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
dx_normj=dc_norm(1,j)
dy_normj=dc_norm(2,j)
dz_normj=dc_norm(3,j)
- xj=c(1,j)+0.5D0*dxj-xmedi
- yj=c(2,j)+0.5D0*dyj-ymedi
- zj=c(3,j)+0.5D0*dzj-zmedi
+C xj=c(1,j)+0.5D0*dxj-xmedi
+C yj=c(2,j)+0.5D0*dyj-ymedi
+C zj=c(3,j)+0.5D0*dzj-zmedi
+ xj=c(1,j)+0.5D0*dxj
+ yj=c(2,j)+0.5D0*dyj
+ zj=c(3,j)+0.5D0*dzj
+ xj=mod(xj,boxxsize)
+ if (xj.lt.0) xj=xj+boxxsize
+ yj=mod(yj,boxysize)
+ if (yj.lt.0) yj=yj+boxysize
+ zj=mod(zj,boxzsize)
+ if (zj.lt.0) zj=zj+boxzsize
+ if ((zj.lt.0).or.(xj.lt.0).or.(yj.lt.0)) write (*,*) "CHUJ"
+ dist_init=(xj-xmedi)**2+(yj-ymedi)**2+(zj-zmedi)**2
+ xj_safe=xj
+ yj_safe=yj
+ zj_safe=zj
+ isubchap=0
+ do xshift=-1,1
+ do yshift=-1,1
+ do zshift=-1,1
+ xj=xj_safe+xshift*boxxsize
+ yj=yj_safe+yshift*boxysize
+ zj=zj_safe+zshift*boxzsize
+ dist_temp=(xj-xmedi)**2+(yj-ymedi)**2+(zj-zmedi)**2
+ if(dist_temp.lt.dist_init) then
+ dist_init=dist_temp
+ xj_temp=xj
+ yj_temp=yj
+ zj_temp=zj
+ isubchap=1
+ endif
+ enddo
+ enddo
+ enddo
+ if (isubchap.eq.1) then
+ xj=xj_temp-xmedi
+ yj=yj_temp-ymedi
+ zj=zj_temp-zmedi
+ else
+ xj=xj_safe-xmedi
+ yj=yj_safe-ymedi
+ zj=zj_safe-zmedi
+ endif
+C if ((i+3).lt.j) then !this condition keeps for turn3 and turn4 not subject to PBC
+c 174 continue
+c if (xj.gt.((0.5d0)*boxxsize)) xj=xj-boxxsize
+c if (xj.lt.((-0.5d0)*boxxsize)) xj=xj+boxxsize
+C Condition for being inside the proper box
+c if ((xj.gt.((0.5d0)*boxxsize)).or.
+c & (xj.lt.((-0.5d0)*boxxsize))) then
+c go to 174
+c endif
+c 175 continue
+c if (yj.gt.((0.5d0)*boxysize)) yj=yj-boxysize
+c if (yj.lt.((-0.5d0)*boxysize)) yj=yj+boxysize
+C Condition for being inside the proper box
+c if ((yj.gt.((0.5d0)*boxysize)).or.
+c & (yj.lt.((-0.5d0)*boxysize))) then
+c go to 175
+c endif
+c 176 continue
+c if (zj.gt.((0.5d0)*boxzsize)) zj=zj-boxzsize
+c if (zj.lt.((-0.5d0)*boxzsize)) zj=zj+boxzsize
+C Condition for being inside the proper box
+c if ((zj.gt.((0.5d0)*boxzsize)).or.
+c & (zj.lt.((-0.5d0)*boxzsize))) then
+c go to 176
+c endif
+C endif !endPBC condintion
+C xj=xj-xmedi
+C yj=yj-ymedi
+C zj=zj-zmedi
rij=xj*xj+yj*yj+zj*zj
+
+ sss=sscale(sqrt(rij))
+ sssgrad=sscagrad(sqrt(rij))
+c if (sss.gt.0.0d0) then
rrmij=1.0D0/rij
rij=dsqrt(rij)
rmij=1.0D0/rij
ev2=bbb*r6ij
fac3=ael6i*r6ij
fac4=ael3i*r3ij
- evdwij=ev1+ev2
+ evdwij=(ev1+ev2)
el1=fac3*(4.0D0+fac*fac-3.0D0*(cosb*cosb+cosg*cosg))
el2=fac4*fac
- eesij=el1+el2
+C MARYSIA
+C eesij=(el1+el2)
C 12/26/95 - for the evaluation of multi-body H-bonding interactions
ees0ij=4.0D0+fac*fac-3.0D0*(cosb*cosb+cosg*cosg)
+ if (shield_mode.gt.0) then
+C fac_shield(i)=0.4
+C fac_shield(j)=0.6
+ el1=el1*fac_shield(i)**2*fac_shield(j)**2
+ el2=el2*fac_shield(i)**2*fac_shield(j)**2
+ eesij=(el1+el2)
+ ees=ees+eesij
+ else
+ fac_shield(i)=1.0
+ fac_shield(j)=1.0
+ eesij=(el1+el2)
ees=ees+eesij
- evdw1=evdw1+evdwij
+ endif
+ evdw1=evdw1+evdwij*sss
cd write(iout,'(2(2i3,2x),7(1pd12.4)/2(3(1pd12.4),5x)/)')
cd & iteli,i,itelj,j,aaa,bbb,ael6i,ael3i,
cd & 1.0D0/dsqrt(rrmij),evdwij,eesij,
cd & xmedi,ymedi,zmedi,xj,yj,zj
if (energy_dec) then
- write (iout,'(a6,2i5,0pf7.3)') 'evdw1',i,j,evdwij
- write (iout,'(a6,2i5,0pf7.3)') 'ees',i,j,eesij
+ write (iout,'(a6,2i5,0pf7.3,2i5,3e11.3)')
+ &'evdw1',i,j,evdwij
+ &,iteli,itelj,aaa,evdw1,sss
+ write (iout,'(a6,2i5,0pf7.3,2f8.3)') 'ees',i,j,eesij,
+ &fac_shield(i),fac_shield(j)
endif
C
C Calculate contributions to the Cartesian gradient.
C
#ifdef SPLITELE
- facvdw=-6*rrmij*(ev1+evdwij)
+ facvdw=-6*rrmij*(ev1+evdwij)*sss
facel=-3*rrmij*(el1+eesij)
fac1=fac
erij(1)=xj*rmij
erij(2)=yj*rmij
erij(3)=zj*rmij
+
*
* 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)
+
*
* Loop over residues i+1 thru j-1.
*
cgrad gelc(l,k)=gelc(l,k)+ggg(l)
cgrad enddo
cgrad enddo
- ggg(1)=facvdw*xj
- ggg(2)=facvdw*yj
- ggg(3)=facvdw*zj
+ if (sss.gt.0.0) then
+ ggg(1)=facvdw*xj+sssgrad*rmij*evdwij*xj
+ ggg(2)=facvdw*yj+sssgrad*rmij*evdwij*yj
+ ggg(3)=facvdw*zj+sssgrad*rmij*evdwij*zj
+ else
+ ggg(1)=0.0
+ ggg(2)=0.0
+ ggg(3)=0.0
+ endif
c do k=1,3
c ghalf=0.5D0*ggg(k)
c gvdwpp(k,i)=gvdwpp(k,i)+ghalf
cgrad enddo
cgrad enddo
#else
- facvdw=ev1+evdwij
- facel=el1+eesij
+C MARYSIA
+ facvdw=(ev1+evdwij)*sss
+ facel=(el1+eesij)
fac1=fac
fac=-3*rrmij*(facvdw+facvdw+facel)
erij(1)=xj*rmij
* 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
cgrad enddo
cgrad enddo
c 9/28/08 AL Gradient compotents will be summed only at the end
- ggg(1)=facvdw*xj
- ggg(2)=facvdw*yj
- ggg(3)=facvdw*zj
+ ggg(1)=facvdw*xj+sssgrad*rmij*evdwij*xj
+ ggg(2)=facvdw*yj+sssgrad*rmij*evdwij*yj
+ ggg(3)=facvdw*zj+sssgrad*rmij*evdwij*zj
do k=1,3
gvdwpp(k,j)=gvdwpp(k,j)+ggg(k)
gvdwpp(k,i)=gvdwpp(k,i)-ggg(k)
cd print '(2i3,2(3(1pd14.5),3x))',i,j,(dcosb(k),k=1,3),
cd & (dcosg(k),k=1,3)
do k=1,3
- ggg(k)=ecosb*dcosb(k)+ecosg*dcosg(k)
+ ggg(k)=(ecosb*dcosb(k)+ecosg*dcosg(k))*
+ & fac_shield(i)**2*fac_shield(j)**2
enddo
c do k=1,3
c ghalf=0.5D0*ggg(k)
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
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
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
& .or. wcorr6.gt.0.0d0 .or. wturn3.gt.0.0d0
& .or. wturn4.gt.0.0d0 .or. wturn6.gt.0.0d0) THEN
C Macromolecules, 1974, 7, 797-806 for definition). This correlation terms
C are computed for EVERY pair of non-contiguous peptide groups.
C
+
if (j.lt.nres-1) then
j1=j+1
j2=j-1
j2=j-2
endif
kkk=0
+ lll=0
do k=1,2
do l=1,2
kkk=kkk+1
muij(kkk)=mu(k,i)*mu(l,j)
+c write(iout,*) 'mumu=', mu(k,i),mu(l,j),i,j,k,l
+#ifdef NEWCORR
+ gmuij1(kkk)=gtb1(k,i+1)*mu(l,j)
+c write(iout,*) 'k=',k,i,gtb1(k,i+1),gtb1(k,i+1)*mu(l,j)
+ gmuij2(kkk)=gUb2(k,i)*mu(l,j)
+ gmuji1(kkk)=mu(k,i)*gtb1(l,j+1)
+c write(iout,*) 'l=',l,j,gtb1(l,j+1),gtb1(l,j+1)*mu(k,i)
+ gmuji2(kkk)=mu(k,i)*gUb2(l,j)
+#endif
enddo
enddo
-cd write (iout,*) 'EELEC: i',i,' j',j
-cd write (iout,*) 'j',j,' j1',j1,' j2',j2
-cd write(iout,*) 'muij',muij
+#ifdef DEBUG
+ write (iout,*) 'EELEC: i',i,' j',j
+ write (iout,*) 'j',j,' j1',j1,' j2',j2
+ write(iout,*) 'muij',muij
+#endif
ury=scalar(uy(1,i),erij)
urz=scalar(uz(1,i),erij)
vry=scalar(uy(1,j),erij)
a32=scalar(uz(1,i),uy(1,j))-3*urz*vry
a33=scalar(uz(1,i),uz(1,j))-3*urz*vrz
fac=dsqrt(-ael6i)*r3ij
+#ifdef DEBUG
+ write (iout,*) "ury",ury," urz",urz," vry",vry," vrz",vrz
+ write (iout,*) "uyvy",scalar(uy(1,i),uy(1,j)),
+ & "uyvz",scalar(uy(1,i),uz(1,j)),
+ & "uzvy",scalar(uz(1,i),uy(1,j)),
+ & "uzvz",scalar(uz(1,i),uz(1,j))
+ write (iout,*) "a22",a22," a23",a23," a32",a32," a33",a33
+ write (iout,*) "fac",fac
+#endif
a22=a22*fac
a23=a23*fac
a32=a32*fac
a33=a33*fac
+#ifdef DEBUG
+ write (iout,*) "a22",a22," a23",a23," a32",a32," a33",a33
+#endif
+#undef DEBUG
cd write (iout,'(4i5,4f10.5)')
cd & i,itortyp(itype(i)),j,itortyp(itype(j)),a22,a23,a32,a33
cd write (iout,'(6f10.5)') (muij(k),k=1,4),fac,eel_loc_ij
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)
+#ifdef DEBUG
+ write (iout,*) "muij",muij," a22",a22," a23",a23," a32",a32,
+ & " a33",a33
+ write (iout,*) "ij",i,j," eel_loc_ij",eel_loc_ij,
+ & " wel_loc",wel_loc
+#endif
+ if (shield_mode.eq.0) then
+ fac_shield(i)=1.0
+ fac_shield(j)=1.0
+C else
+C fac_shield(i)=0.4
+C fac_shield(j)=0.6
+ endif
+ eel_loc_ij=eel_loc_ij
+ & *fac_shield(i)*fac_shield(j)
+c if (energy_dec) write (iout,'(a6,2i5,0pf7.3)')
+c & 'eelloc',i,j,eel_loc_ij
+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=',i,j,muij(1),muij(2),muij(3),muij(4)
+C Calculate patrial derivative for theta angle
+#ifdef NEWCORR
+ geel_loc_ij=(a22*gmuij1(1)
+ & +a23*gmuij1(2)
+ & +a32*gmuij1(3)
+ & +a33*gmuij1(4))
+ & *fac_shield(i)*fac_shield(j)
+c write(iout,*) "derivative over thatai"
+c write(iout,*) a22*gmuij1(1), a23*gmuij1(2) ,a32*gmuij1(3),
+c & a33*gmuij1(4)
+ gloc(nphi+i,icg)=gloc(nphi+i,icg)+
+ & geel_loc_ij*wel_loc
+c write(iout,*) "derivative over thatai-1"
+c write(iout,*) a22*gmuij2(1), a23*gmuij2(2) ,a32*gmuij2(3),
+c & a33*gmuij2(4)
+ geel_loc_ij=
+ & a22*gmuij2(1)
+ & +a23*gmuij2(2)
+ & +a32*gmuij2(3)
+ & +a33*gmuij2(4)
+ gloc(nphi+i-1,icg)=gloc(nphi+i-1,icg)+
+ & geel_loc_ij*wel_loc
+ & *fac_shield(i)*fac_shield(j)
+
+c Derivative over j residue
+ geel_loc_ji=a22*gmuji1(1)
+ & +a23*gmuji1(2)
+ & +a32*gmuji1(3)
+ & +a33*gmuji1(4)
+c write(iout,*) "derivative over thataj"
+c write(iout,*) a22*gmuji1(1), a23*gmuji1(2) ,a32*gmuji1(3),
+c & a33*gmuji1(4)
+
+ gloc(nphi+j,icg)=gloc(nphi+j,icg)+
+ & geel_loc_ji*wel_loc
+ & *fac_shield(i)*fac_shield(j)
+
+ geel_loc_ji=
+ & +a22*gmuji2(1)
+ & +a23*gmuji2(2)
+ & +a32*gmuji2(3)
+ & +a33*gmuji2(4)
+c write(iout,*) "derivative over thataj-1"
+c write(iout,*) a22*gmuji2(1), a23*gmuji2(2) ,a32*gmuji2(3),
+c & a33*gmuji2(4)
+ gloc(nphi+j-1,icg)=gloc(nphi+j-1,icg)+
+ & geel_loc_ji*wel_loc
+ & *fac_shield(i)*fac_shield(j)
+#endif
cd write (iout,*) 'i',i,' j',j,' eel_loc_ij',eel_loc_ij
if (energy_dec) write (iout,'(a6,2i5,0pf7.3)')
& 'eelloc',i,j,eel_loc_ij
+c if (eel_loc_ij.ne.0)
+c & write (iout,'(a4,2i4,8f9.5)')'chuj',
+c & i,j,a22,muij(1),a23,muij(2),a32,muij(3),a33,muij(4)
eel_loc=eel_loc+eel_loc_ij
C Partial derivatives in virtual-bond dihedral angles gamma
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)
+
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)
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)
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 enddo
C Remaining derivatives of eello
do l=1,3
- gel_loc(l,i)=gel_loc(l,i)+aggi(l,1)*muij(1)+
- & aggi(l,2)*muij(2)+aggi(l,3)*muij(3)+aggi(l,4)*muij(4)
- gel_loc(l,i+1)=gel_loc(l,i+1)+aggi1(l,1)*muij(1)+
- & aggi1(l,2)*muij(2)+aggi1(l,3)*muij(3)+aggi1(l,4)*muij(4)
- gel_loc(l,j)=gel_loc(l,j)+aggj(l,1)*muij(1)+
- & aggj(l,2)*muij(2)+aggj(l,3)*muij(3)+aggj(l,4)*muij(4)
- gel_loc(l,j1)=gel_loc(l,j1)+aggj1(l,1)*muij(1)+
- & aggj1(l,2)*muij(2)+aggj1(l,3)*muij(3)+aggj1(l,4)*muij(4)
+ gel_loc(l,i)=gel_loc(l,i)+(aggi(l,1)*muij(1)+
+ & aggi(l,2)*muij(2)+aggi(l,3)*muij(3)+aggi(l,4)*muij(4))
+ & *fac_shield(i)*fac_shield(j)
+
+ gel_loc(l,i+1)=gel_loc(l,i+1)+(aggi1(l,1)*muij(1)+
+ & aggi1(l,2)*muij(2)+aggi1(l,3)*muij(3)+aggi1(l,4)*muij(4))
+ & *fac_shield(i)*fac_shield(j)
+
+ gel_loc(l,j)=gel_loc(l,j)+(aggj(l,1)*muij(1)+
+ & aggj(l,2)*muij(2)+aggj(l,3)*muij(3)+aggj(l,4)*muij(4))
+ & *fac_shield(i)*fac_shield(j)
+
+ gel_loc(l,j1)=gel_loc(l,j1)+(aggj1(l,1)*muij(1)+
+ & aggj1(l,2)*muij(2)+aggj1(l,3)*muij(3)+aggj1(l,4)*muij(4))
+ & *fac_shield(i)*fac_shield(j)
+
enddo
ENDIF
C Change 12/26/95 to calculate four-body contributions to H-bonding energy
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
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
include 'COMMON.VECTORS'
include 'COMMON.FFIELD'
include 'COMMON.CONTROL'
+ include 'COMMON.SHIELD'
dimension ggg(3)
double precision auxmat(2,2),auxmat1(2,2),auxmat2(2,2),pizda(2,2),
& e1t(2,2),e2t(2,2),e3t(2,2),e1tder(2,2),e2tder(2,2),e3tder(2,2),
- & e1a(2,2),ae3(2,2),ae3e2(2,2),auxvec(2),auxvec1(2)
+ & e1a(2,2),ae3(2,2),ae3e2(2,2),auxvec(2),auxvec1(2),gpizda1(2,2),
+ & gpizda2(2,2),auxgmat1(2,2),auxgmatt1(2,2),
+ & auxgmat2(2,2),auxgmatt2(2,2)
double precision agg(3,4),aggi(3,4),aggi1(3,4),
& aggj(3,4),aggj1(3,4),a_temp(2,2),auxmat3(2,2)
common /locel/ a_temp,agg,aggi,aggi1,aggj,aggj1,a22,a23,a32,a33,
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
cd call checkint_turn3(i,a_temp,eello_turn3_num)
call matmat2(EUg(1,1,i+1),EUg(1,1,i+2),auxmat(1,1))
+c auxalary matices for theta gradient
+c auxalary matrix for i+1 and constant i+2
+ call matmat2(gtEUg(1,1,i+1),EUg(1,1,i+2),auxgmat1(1,1))
+c auxalary matrix for i+2 and constant i+1
+ call matmat2(EUg(1,1,i+1),gtEUg(1,1,i+2),auxgmat2(1,1))
call transpose2(auxmat(1,1),auxmat1(1,1))
+ call transpose2(auxgmat1(1,1),auxgmatt1(1,1))
+ call transpose2(auxgmat2(1,1),auxgmatt2(1,1))
call matmat2(a_temp(1,1),auxmat1(1,1),pizda(1,1))
+ call matmat2(a_temp(1,1),auxgmatt1(1,1),gpizda1(1,1))
+ call matmat2(a_temp(1,1),auxgmatt2(1,1),gpizda2(1,1))
+ if (shield_mode.eq.0) then
+ fac_shield(i)=1.0
+ fac_shield(j)=1.0
+C else
+C fac_shield(i)=0.4
+C fac_shield(j)=0.6
+ endif
eello_turn3=eello_turn3+0.5d0*(pizda(1,1)+pizda(2,2))
- if (energy_dec) write (iout,'(a6,2i5,0pf7.3)')
- & 'eturn3',i,j,0.5d0*(pizda(1,1)+pizda(2,2))
+ & *fac_shield(i)*fac_shield(j)
+ eello_t3=0.5d0*(pizda(1,1)+pizda(2,2))
+ & *fac_shield(i)*fac_shield(j)
+ if (energy_dec) write (iout,'(6heturn3,2i5,0pf7.3)') i,i+2,
+ & eello_t3
+C#ifdef NEWCORR
+C Derivatives in theta
+ gloc(nphi+i,icg)=gloc(nphi+i,icg)
+ & +0.5d0*(gpizda1(1,1)+gpizda1(2,2))*wturn3
+ & *fac_shield(i)*fac_shield(j)
+ gloc(nphi+i+1,icg)=gloc(nphi+i+1,icg)
+ & +0.5d0*(gpizda2(1,1)+gpizda2(2,2))*wturn3
+ & *fac_shield(i)*fac_shield(j)
+C#endif
+
+C Derivatives in shield mode
+ if ((fac_shield(i).gt.0).and.(fac_shield(j).gt.0).and.
+ & (shield_mode.gt.0)) then
+C print *,i,j
+
+ do ilist=1,ishield_list(i)
+ iresshield=shield_list(ilist,i)
+ do k=1,3
+ rlocshield=grad_shield_side(k,ilist,i)*eello_t3/fac_shield(i)
+C & *2.0
+ gshieldx_t3(k,iresshield)=gshieldx_t3(k,iresshield)+
+ & rlocshield
+ & +grad_shield_loc(k,ilist,i)*eello_t3/fac_shield(i)
+ gshieldc_t3(k,iresshield-1)=gshieldc_t3(k,iresshield-1)
+ & +rlocshield
+ enddo
+ enddo
+ do ilist=1,ishield_list(j)
+ iresshield=shield_list(ilist,j)
+ do k=1,3
+ rlocshield=grad_shield_side(k,ilist,j)*eello_t3/fac_shield(j)
+C & *2.0
+ gshieldx_t3(k,iresshield)=gshieldx_t3(k,iresshield)+
+ & rlocshield
+ & +grad_shield_loc(k,ilist,j)*eello_t3/fac_shield(j)
+ gshieldc_t3(k,iresshield-1)=gshieldc_t3(k,iresshield-1)
+ & +rlocshield
+
+ enddo
+ enddo
+
+ do k=1,3
+ gshieldc_t3(k,i)=gshieldc_t3(k,i)+
+ & grad_shield(k,i)*eello_t3/fac_shield(i)
+ gshieldc_t3(k,j)=gshieldc_t3(k,j)+
+ & grad_shield(k,j)*eello_t3/fac_shield(j)
+ gshieldc_t3(k,i-1)=gshieldc_t3(k,i-1)+
+ & grad_shield(k,i)*eello_t3/fac_shield(i)
+ gshieldc_t3(k,j-1)=gshieldc_t3(k,j-1)+
+ & grad_shield(k,j)*eello_t3/fac_shield(j)
+ enddo
+ endif
+
+C if (energy_dec) write (iout,'(a6,2i5,0pf7.3)')
cd write (2,*) 'i,',i,' j',j,'eello_turn3',
cd & 0.5d0*(pizda(1,1)+pizda(2,2)),
cd & ' eello_turn3_num',4*eello_turn3_num
call transpose2(auxmat2(1,1),auxmat3(1,1))
call matmat2(a_temp(1,1),auxmat3(1,1),pizda(1,1))
gel_loc_turn3(i)=gel_loc_turn3(i)+0.5d0*(pizda(1,1)+pizda(2,2))
+ & *fac_shield(i)*fac_shield(j)
C Derivatives in gamma(i+1)
call matmat2(EUg(1,1,i+1),EUgder(1,1,i+2),auxmat2(1,1))
call transpose2(auxmat2(1,1),auxmat3(1,1))
call matmat2(a_temp(1,1),auxmat3(1,1),pizda(1,1))
gel_loc_turn3(i+1)=gel_loc_turn3(i+1)
& +0.5d0*(pizda(1,1)+pizda(2,2))
+ & *fac_shield(i)*fac_shield(j)
C Cartesian derivatives
do l=1,3
c ghalf1=0.5d0*agg(l,1)
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)
+
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)
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)
a_temp(1,1)=aggj(l,1)!+ghalf1
a_temp(1,2)=aggj(l,2)!+ghalf2
a_temp(2,1)=aggj(l,3)!+ghalf3
call matmat2(a_temp(1,1),auxmat1(1,1),pizda(1,1))
gcorr3_turn(l,j)=gcorr3_turn(l,j)
& +0.5d0*(pizda(1,1)+pizda(2,2))
+ & *fac_shield(i)*fac_shield(j)
a_temp(1,1)=aggj1(l,1)
a_temp(1,2)=aggj1(l,2)
a_temp(2,1)=aggj1(l,3)
call matmat2(a_temp(1,1),auxmat1(1,1),pizda(1,1))
gcorr3_turn(l,j1)=gcorr3_turn(l,j1)
& +0.5d0*(pizda(1,1)+pizda(2,2))
+ & *fac_shield(i)*fac_shield(j)
enddo
return
end
include 'COMMON.VECTORS'
include 'COMMON.FFIELD'
include 'COMMON.CONTROL'
+ include 'COMMON.SHIELD'
dimension ggg(3)
double precision auxmat(2,2),auxmat1(2,2),auxmat2(2,2),pizda(2,2),
& e1t(2,2),e2t(2,2),e3t(2,2),e1tder(2,2),e2tder(2,2),e3tder(2,2),
- & e1a(2,2),ae3(2,2),ae3e2(2,2),auxvec(2),auxvec1(2)
+ & e1a(2,2),ae3(2,2),ae3e2(2,2),auxvec(2),auxvec1(2),auxgvec(2),
+ & auxgEvec1(2),auxgEvec2(2),auxgEvec3(2),
+ & gte1t(2,2),gte2t(2,2),gte3t(2,2),
+ & gte1a(2,2),gtae3(2,2),gtae3e2(2,2), ae3gte2(2,2),
+ & gtEpizda1(2,2),gtEpizda2(2,2),gtEpizda3(2,2)
double precision agg(3,4),aggi(3,4),aggi1(3,4),
& aggj(3,4),aggj1(3,4),a_temp(2,2),auxmat3(2,2)
common /locel/ a_temp,agg,aggi,aggi1,aggj,aggj1,a22,a23,a32,a33,
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"
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))
call transpose2(Eug(1,1,i+3),e3t(1,1))
+C Ematrix derivative in theta
+ call transpose2(gtEUg(1,1,i+1),gte1t(1,1))
+ call transpose2(gtEug(1,1,i+2),gte2t(1,1))
+ call transpose2(gtEug(1,1,i+3),gte3t(1,1))
call matmat2(e1t(1,1),a_temp(1,1),e1a(1,1))
+c eta1 in derivative theta
+ call matmat2(gte1t(1,1),a_temp(1,1),gte1a(1,1))
call matvec2(e1a(1,1),Ub2(1,i+3),auxvec(1))
- s1=scalar2(b1(1,iti2),auxvec(1))
+c auxgvec is derivative of Ub2 so i+3 theta
+ call matvec2(e1a(1,1),gUb2(1,i+3),auxgvec(1))
+c auxalary matrix of E i+1
+ call matvec2(gte1a(1,1),Ub2(1,i+3),auxgEvec1(1))
+c s1=0.0
+c gs1=0.0
+ s1=scalar2(b1(1,i+2),auxvec(1))
+c derivative of theta i+2 with constant i+3
+ gs23=scalar2(gtb1(1,i+2),auxvec(1))
+c derivative of theta i+2 with constant i+2
+ gs32=scalar2(b1(1,i+2),auxgvec(1))
+c derivative of E matix in theta of i+1
+ gsE13=scalar2(b1(1,i+2),auxgEvec1(1))
+
call matmat2(a_temp(1,1),e3t(1,1),ae3(1,1))
+c ea31 in derivative theta
+ call matmat2(a_temp(1,1),gte3t(1,1),gtae3(1,1))
call matvec2(ae3(1,1),Ub2(1,i+2),auxvec(1))
- s2=scalar2(b1(1,iti1),auxvec(1))
+c auxilary matrix auxgvec of Ub2 with constant E matirx
+ call matvec2(ae3(1,1),gUb2(1,i+2),auxgvec(1))
+c auxilary matrix auxgEvec1 of E matix with Ub2 constant
+ call matvec2(gtae3(1,1),Ub2(1,i+2),auxgEvec3(1))
+
+c s2=0.0
+c gs2=0.0
+ s2=scalar2(b1(1,i+1),auxvec(1))
+c derivative of theta i+1 with constant i+3
+ gs13=scalar2(gtb1(1,i+1),auxvec(1))
+c derivative of theta i+2 with constant i+1
+ gs21=scalar2(b1(1,i+1),auxgvec(1))
+c derivative of theta i+3 with constant i+1
+ gsE31=scalar2(b1(1,i+1),auxgEvec3(1))
+c write(iout,*) gs1,gs2,'i=',i,auxgvec(1),gUb2(1,i+2),gtb1(1,i+2),
+c & gtb1(1,i+1)
call matmat2(ae3(1,1),e2t(1,1),ae3e2(1,1))
+c two derivatives over diffetent matrices
+c gtae3e2 is derivative over i+3
+ call matmat2(gtae3(1,1),e2t(1,1),gtae3e2(1,1))
+c ae3gte2 is derivative over i+2
+ call matmat2(ae3(1,1),gte2t(1,1),ae3gte2(1,1))
call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1))
+c three possible derivative over theta E matices
+c i+1
+ call matmat2(ae3e2(1,1),gte1t(1,1),gtEpizda1(1,1))
+c i+2
+ call matmat2(ae3gte2(1,1),e1t(1,1),gtEpizda2(1,1))
+c i+3
+ call matmat2(gtae3e2(1,1),e1t(1,1),gtEpizda3(1,1))
s3=0.5d0*(pizda(1,1)+pizda(2,2))
+
+ gsEE1=0.5d0*(gtEpizda1(1,1)+gtEpizda1(2,2))
+ gsEE2=0.5d0*(gtEpizda2(1,1)+gtEpizda2(2,2))
+ gsEE3=0.5d0*(gtEpizda3(1,1)+gtEpizda3(2,2))
+ if (shield_mode.eq.0) then
+ fac_shield(i)=1.0
+ fac_shield(j)=1.0
+C else
+C fac_shield(i)=0.6
+C fac_shield(j)=0.4
+ endif
eello_turn4=eello_turn4-(s1+s2+s3)
- if (energy_dec) write (iout,'(a6,2i5,0pf7.3)')
- & 'eturn4',i,j,-(s1+s2+s3)
-cd write (2,*) 'i,',i,' j',j,'eello_turn4',-(s1+s2+s3),
-cd & ' eello_turn4_num',8*eello_turn4_num
+ & *fac_shield(i)*fac_shield(j)
+ eello_t4=-(s1+s2+s3)
+ & *fac_shield(i)*fac_shield(j)
+c write(iout,*)'chujOWO', auxvec(1),b1(1,iti2)
+ if (energy_dec) write (iout,'(a6,2i5,0pf7.3,3f7.3)')
+ & 'eturn4',i,j,-(s1+s2+s3),s1,s2,s3
+C Now derivative over shield:
+ if ((fac_shield(i).gt.0).and.(fac_shield(j).gt.0).and.
+ & (shield_mode.gt.0)) then
+C print *,i,j
+
+ do ilist=1,ishield_list(i)
+ iresshield=shield_list(ilist,i)
+ do k=1,3
+ rlocshield=grad_shield_side(k,ilist,i)*eello_t4/fac_shield(i)
+C & *2.0
+ gshieldx_t4(k,iresshield)=gshieldx_t4(k,iresshield)+
+ & rlocshield
+ & +grad_shield_loc(k,ilist,i)*eello_t4/fac_shield(i)
+ gshieldc_t4(k,iresshield-1)=gshieldc_t4(k,iresshield-1)
+ & +rlocshield
+ enddo
+ enddo
+ do ilist=1,ishield_list(j)
+ iresshield=shield_list(ilist,j)
+ do k=1,3
+ rlocshield=grad_shield_side(k,ilist,j)*eello_t4/fac_shield(j)
+C & *2.0
+ gshieldx_t4(k,iresshield)=gshieldx_t4(k,iresshield)+
+ & rlocshield
+ & +grad_shield_loc(k,ilist,j)*eello_t4/fac_shield(j)
+ gshieldc_t4(k,iresshield-1)=gshieldc_t4(k,iresshield-1)
+ & +rlocshield
+
+ enddo
+ enddo
+
+ do k=1,3
+ gshieldc_t4(k,i)=gshieldc_t4(k,i)+
+ & grad_shield(k,i)*eello_t4/fac_shield(i)
+ gshieldc_t4(k,j)=gshieldc_t4(k,j)+
+ & grad_shield(k,j)*eello_t4/fac_shield(j)
+ gshieldc_t4(k,i-1)=gshieldc_t4(k,i-1)+
+ & grad_shield(k,i)*eello_t4/fac_shield(i)
+ gshieldc_t4(k,j-1)=gshieldc_t4(k,j-1)+
+ & grad_shield(k,j)*eello_t4/fac_shield(j)
+ enddo
+ endif
+
+
+
+
+
+
+cd write (2,*) 'i,',i,' j',j,'eello_turn4',-(s1+s2+s3),
+cd & ' eello_turn4_num',8*eello_turn4_num
+#ifdef NEWCORR
+ gloc(nphi+i,icg)=gloc(nphi+i,icg)
+ & -(gs13+gsE13+gsEE1)*wturn4
+ & *fac_shield(i)*fac_shield(j)
+ gloc(nphi+i+1,icg)= gloc(nphi+i+1,icg)
+ & -(gs23+gs21+gsEE2)*wturn4
+ & *fac_shield(i)*fac_shield(j)
+
+ gloc(nphi+i+2,icg)= gloc(nphi+i+2,icg)
+ & -(gs32+gsE31+gsEE3)*wturn4
+ & *fac_shield(i)*fac_shield(j)
+
+c gloc(nphi+i+1,icg)=gloc(nphi+i+1,icg)-
+c & gs2
+#endif
+ if (energy_dec) write (iout,'(a6,2i5,0pf7.3)')
+ & 'eturn4',i,j,-(s1+s2+s3)
+c write (iout,*) 'i,',i,' j',j,'eello_turn4',-(s1+s2+s3),
+c & ' eello_turn4_num',8*eello_turn4_num
C Derivatives in gamma(i)
call transpose2(EUgder(1,1,i+1),e1tder(1,1))
call matmat2(e1tder(1,1),a_temp(1,1),auxmat(1,1))
call matvec2(auxmat(1,1),Ub2(1,i+3),auxvec(1))
- s1=scalar2(b1(1,iti2),auxvec(1))
+ s1=scalar2(b1(1,i+2),auxvec(1))
call matmat2(ae3e2(1,1),e1tder(1,1),pizda(1,1))
s3=0.5d0*(pizda(1,1)+pizda(2,2))
gel_loc_turn4(i)=gel_loc_turn4(i)-(s1+s3)
+ & *fac_shield(i)*fac_shield(j)
C Derivatives in gamma(i+1)
call transpose2(EUgder(1,1,i+2),e2tder(1,1))
call matvec2(ae3(1,1),Ub2der(1,i+2),auxvec(1))
- s2=scalar2(b1(1,iti1),auxvec(1))
+ s2=scalar2(b1(1,i+1),auxvec(1))
call matmat2(ae3(1,1),e2tder(1,1),auxmat(1,1))
call matmat2(auxmat(1,1),e1t(1,1),pizda(1,1))
s3=0.5d0*(pizda(1,1)+pizda(2,2))
gel_loc_turn4(i+1)=gel_loc_turn4(i+1)-(s2+s3)
+ & *fac_shield(i)*fac_shield(j)
C Derivatives in gamma(i+2)
call transpose2(EUgder(1,1,i+3),e3tder(1,1))
call matvec2(e1a(1,1),Ub2der(1,i+3),auxvec(1))
- s1=scalar2(b1(1,iti2),auxvec(1))
+ s1=scalar2(b1(1,i+2),auxvec(1))
call matmat2(a_temp(1,1),e3tder(1,1),auxmat(1,1))
call matvec2(auxmat(1,1),Ub2(1,i+2),auxvec(1))
- s2=scalar2(b1(1,iti1),auxvec(1))
+ s2=scalar2(b1(1,i+1),auxvec(1))
call matmat2(auxmat(1,1),e2t(1,1),auxmat3(1,1))
call matmat2(auxmat3(1,1),e1t(1,1),pizda(1,1))
s3=0.5d0*(pizda(1,1)+pizda(2,2))
gel_loc_turn4(i+2)=gel_loc_turn4(i+2)-(s1+s2+s3)
+ & *fac_shield(i)*fac_shield(j)
C Cartesian derivatives
C Derivatives of this turn contributions in DC(i+2)
if (j.lt.nres-1) then
a_temp(2,2)=agg(l,4)
call matmat2(e1t(1,1),a_temp(1,1),e1a(1,1))
call matvec2(e1a(1,1),Ub2(1,i+3),auxvec(1))
- s1=scalar2(b1(1,iti2),auxvec(1))
+ s1=scalar2(b1(1,i+2),auxvec(1))
call matmat2(a_temp(1,1),e3t(1,1),ae3(1,1))
call matvec2(ae3(1,1),Ub2(1,i+2),auxvec(1))
- s2=scalar2(b1(1,iti1),auxvec(1))
+ s2=scalar2(b1(1,i+1),auxvec(1))
call matmat2(ae3(1,1),e2t(1,1),ae3e2(1,1))
call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1))
s3=0.5d0*(pizda(1,1)+pizda(2,2))
ggg(l)=-(s1+s2+s3)
gcorr4_turn(l,i+2)=gcorr4_turn(l,i+2)-(s1+s2+s3)
+ & *fac_shield(i)*fac_shield(j)
enddo
endif
C Remaining derivatives of this turn contribution
a_temp(2,2)=aggi(l,4)
call matmat2(e1t(1,1),a_temp(1,1),e1a(1,1))
call matvec2(e1a(1,1),Ub2(1,i+3),auxvec(1))
- s1=scalar2(b1(1,iti2),auxvec(1))
+ s1=scalar2(b1(1,i+2),auxvec(1))
call matmat2(a_temp(1,1),e3t(1,1),ae3(1,1))
call matvec2(ae3(1,1),Ub2(1,i+2),auxvec(1))
- s2=scalar2(b1(1,iti1),auxvec(1))
+ s2=scalar2(b1(1,i+1),auxvec(1))
call matmat2(ae3(1,1),e2t(1,1),ae3e2(1,1))
call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1))
s3=0.5d0*(pizda(1,1)+pizda(2,2))
gcorr4_turn(l,i)=gcorr4_turn(l,i)-(s1+s2+s3)
+ & *fac_shield(i)*fac_shield(j)
a_temp(1,1)=aggi1(l,1)
a_temp(1,2)=aggi1(l,2)
a_temp(2,1)=aggi1(l,3)
a_temp(2,2)=aggi1(l,4)
call matmat2(e1t(1,1),a_temp(1,1),e1a(1,1))
call matvec2(e1a(1,1),Ub2(1,i+3),auxvec(1))
- s1=scalar2(b1(1,iti2),auxvec(1))
+ s1=scalar2(b1(1,i+2),auxvec(1))
call matmat2(a_temp(1,1),e3t(1,1),ae3(1,1))
call matvec2(ae3(1,1),Ub2(1,i+2),auxvec(1))
- s2=scalar2(b1(1,iti1),auxvec(1))
+ s2=scalar2(b1(1,i+1),auxvec(1))
call matmat2(ae3(1,1),e2t(1,1),ae3e2(1,1))
call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1))
s3=0.5d0*(pizda(1,1)+pizda(2,2))
gcorr4_turn(l,i+1)=gcorr4_turn(l,i+1)-(s1+s2+s3)
+ & *fac_shield(i)*fac_shield(j)
a_temp(1,1)=aggj(l,1)
a_temp(1,2)=aggj(l,2)
a_temp(2,1)=aggj(l,3)
a_temp(2,2)=aggj(l,4)
call matmat2(e1t(1,1),a_temp(1,1),e1a(1,1))
call matvec2(e1a(1,1),Ub2(1,i+3),auxvec(1))
- s1=scalar2(b1(1,iti2),auxvec(1))
+ s1=scalar2(b1(1,i+2),auxvec(1))
call matmat2(a_temp(1,1),e3t(1,1),ae3(1,1))
call matvec2(ae3(1,1),Ub2(1,i+2),auxvec(1))
- s2=scalar2(b1(1,iti1),auxvec(1))
+ s2=scalar2(b1(1,i+1),auxvec(1))
call matmat2(ae3(1,1),e2t(1,1),ae3e2(1,1))
call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1))
s3=0.5d0*(pizda(1,1)+pizda(2,2))
gcorr4_turn(l,j)=gcorr4_turn(l,j)-(s1+s2+s3)
+ & *fac_shield(i)*fac_shield(j)
a_temp(1,1)=aggj1(l,1)
a_temp(1,2)=aggj1(l,2)
a_temp(2,1)=aggj1(l,3)
a_temp(2,2)=aggj1(l,4)
call matmat2(e1t(1,1),a_temp(1,1),e1a(1,1))
call matvec2(e1a(1,1),Ub2(1,i+3),auxvec(1))
- s1=scalar2(b1(1,iti2),auxvec(1))
+ s1=scalar2(b1(1,i+2),auxvec(1))
call matmat2(a_temp(1,1),e3t(1,1),ae3(1,1))
call matvec2(ae3(1,1),Ub2(1,i+2),auxvec(1))
- s2=scalar2(b1(1,iti1),auxvec(1))
+ s2=scalar2(b1(1,i+1),auxvec(1))
call matmat2(ae3(1,1),e2t(1,1),ae3e2(1,1))
call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1))
s3=0.5d0*(pizda(1,1)+pizda(2,2))
c write (iout,*) "s1",s1," s2",s2," s3",s3," s1+s2+s3",s1+s2+s3
gcorr4_turn(l,j1)=gcorr4_turn(l,j1)-(s1+s2+s3)
+ & *fac_shield(i)*fac_shield(j)
enddo
return
end
include 'COMMON.IOUNITS'
include 'COMMON.CONTROL'
dimension ggg(3)
+ integer xshift,yshift,zshift
evdw2=0.0D0
evdw2_14=0.0d0
r0_scp=4.5d0
cd print '(a)','Enter ESCP'
cd write (iout,*) 'iatscp_s=',iatscp_s,' iatscp_e=',iatscp_e
+C do xshift=-1,1
+C do yshift=-1,1
+C do zshift=-1,1
do i=iatscp_s,iatscp_e
- if (itype(i).eq.21 .or. itype(i+1).eq.21) cycle
+ if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle
iteli=itel(i)
xi=0.5D0*(c(1,i)+c(1,i+1))
yi=0.5D0*(c(2,i)+c(2,i+1))
zi=0.5D0*(c(3,i)+c(3,i+1))
-
+C Return atom into box, boxxsize is size of box in x dimension
+c 134 continue
+c if (xi.gt.((xshift+0.5d0)*boxxsize)) xi=xi-boxxsize
+c if (xi.lt.((xshift-0.5d0)*boxxsize)) xi=xi+boxxsize
+C Condition for being inside the proper box
+c if ((xi.gt.((xshift+0.5d0)*boxxsize)).or.
+c & (xi.lt.((xshift-0.5d0)*boxxsize))) then
+c go to 134
+c endif
+c 135 continue
+c if (yi.gt.((yshift+0.5d0)*boxysize)) yi=yi-boxysize
+c if (yi.lt.((yshift-0.5d0)*boxysize)) yi=yi+boxysize
+C Condition for being inside the proper box
+c if ((yi.gt.((yshift+0.5d0)*boxysize)).or.
+c & (yi.lt.((yshift-0.5d0)*boxysize))) then
+c go to 135
+c c endif
+c 136 continue
+c if (zi.gt.((zshift+0.5d0)*boxzsize)) zi=zi-boxzsize
+c if (zi.lt.((zshift-0.5d0)*boxzsize)) zi=zi+boxzsize
+cC Condition for being inside the proper box
+c if ((zi.gt.((zshift+0.5d0)*boxzsize)).or.
+c & (zi.lt.((zshift-0.5d0)*boxzsize))) then
+c go to 136
+c endif
+ xi=mod(xi,boxxsize)
+ if (xi.lt.0) xi=xi+boxxsize
+ yi=mod(yi,boxysize)
+ if (yi.lt.0) yi=yi+boxysize
+ zi=mod(zi,boxzsize)
+ if (zi.lt.0) zi=zi+boxzsize
+C xi=xi+xshift*boxxsize
+C yi=yi+yshift*boxysize
+C zi=zi+zshift*boxzsize
do iint=1,nscp_gr(i)
do j=iscpstart(i,iint),iscpend(i,iint)
- if (itype(j).eq.21) cycle
- itypj=itype(j)
+ if (itype(j).eq.ntyp1) cycle
+ itypj=iabs(itype(j))
C Uncomment following three lines for SC-p interactions
c xj=c(1,nres+j)-xi
c yj=c(2,nres+j)-yi
c zj=c(3,nres+j)-zi
C Uncomment following three lines for Ca-p interactions
- xj=c(1,j)-xi
- yj=c(2,j)-yi
- zj=c(3,j)-zi
+ xj=c(1,j)
+ yj=c(2,j)
+ zj=c(3,j)
+c 174 continue
+c if (xj.gt.((0.5d0)*boxxsize)) xj=xj-boxxsize
+c if (xj.lt.((-0.5d0)*boxxsize)) xj=xj+boxxsize
+C Condition for being inside the proper box
+c if ((xj.gt.((0.5d0)*boxxsize)).or.
+c & (xj.lt.((-0.5d0)*boxxsize))) then
+c go to 174
+c endif
+c 175 continue
+c if (yj.gt.((0.5d0)*boxysize)) yj=yj-boxysize
+c if (yj.lt.((-0.5d0)*boxysize)) yj=yj+boxysize
+cC Condition for being inside the proper box
+c if ((yj.gt.((0.5d0)*boxysize)).or.
+c & (yj.lt.((-0.5d0)*boxysize))) then
+c go to 175
+c endif
+c 176 continue
+c if (zj.gt.((0.5d0)*boxzsize)) zj=zj-boxzsize
+c if (zj.lt.((-0.5d0)*boxzsize)) zj=zj+boxzsize
+C Condition for being inside the proper box
+c if ((zj.gt.((0.5d0)*boxzsize)).or.
+c & (zj.lt.((-0.5d0)*boxzsize))) then
+c go to 176
+ xj=mod(xj,boxxsize)
+ if (xj.lt.0) xj=xj+boxxsize
+ yj=mod(yj,boxysize)
+ if (yj.lt.0) yj=yj+boxysize
+ zj=mod(zj,boxzsize)
+ if (zj.lt.0) zj=zj+boxzsize
+ dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
+ xj_safe=xj
+ yj_safe=yj
+ zj_safe=zj
+ subchap=0
+ do xshift=-1,1
+ do yshift=-1,1
+ do zshift=-1,1
+ xj=xj_safe+xshift*boxxsize
+ yj=yj_safe+yshift*boxysize
+ zj=zj_safe+zshift*boxzsize
+ dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
+ if(dist_temp.lt.dist_init) then
+ dist_init=dist_temp
+ xj_temp=xj
+ yj_temp=yj
+ zj_temp=zj
+ subchap=1
+ endif
+ enddo
+ enddo
+ enddo
+ if (subchap.eq.1) then
+ xj=xj_temp-xi
+ yj=yj_temp-yi
+ zj=zj_temp-zi
+ else
+ xj=xj_safe-xi
+ yj=yj_safe-yi
+ zj=zj_safe-zi
+ endif
+c c endif
+C xj=xj-xi
+C yj=yj-yi
+C zj=zj-zi
rij=xj*xj+yj*yj+zj*zj
+
r0ij=r0_scp
r0ijsq=r0ij*r0ij
if (rij.lt.r0ijsq) then
enddo ! iint
enddo ! i
+C enddo !zshift
+C enddo !yshift
+C enddo !xshift
return
end
C-----------------------------------------------------------------------------
include 'COMMON.FFIELD'
include 'COMMON.IOUNITS'
include 'COMMON.CONTROL'
+ include 'COMMON.SPLITELE'
+ integer xshift,yshift,zshift
dimension ggg(3)
evdw2=0.0D0
evdw2_14=0.0d0
+c print *,boxxsize,boxysize,boxzsize,'wymiary pudla'
cd print '(a)','Enter ESCP'
cd write (iout,*) 'iatscp_s=',iatscp_s,' iatscp_e=',iatscp_e
+C do xshift=-1,1
+C do yshift=-1,1
+C do zshift=-1,1
+c write (iout,*) "INIgvdwc_scp"
+c do i=1,nres
+c write (iout,'(i5,3f10.5,5x,3f10.5)') i,(gvdwc_scp(j,i),j=1,3),
+c & (gvdwc_scpp(j,i),j=1,3)
+c enddo
+ if (energy_dec) write (iout,*) "escp:",r_cut,rlamb
do i=iatscp_s,iatscp_e
- if (itype(i).eq.21 .or. itype(i+1).eq.21) cycle
+ if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle
iteli=itel(i)
xi=0.5D0*(c(1,i)+c(1,i+1))
yi=0.5D0*(c(2,i)+c(2,i+1))
zi=0.5D0*(c(3,i)+c(3,i+1))
+ xi=mod(xi,boxxsize)
+ if (xi.lt.0) xi=xi+boxxsize
+ yi=mod(yi,boxysize)
+ if (yi.lt.0) yi=yi+boxysize
+ zi=mod(zi,boxzsize)
+ if (zi.lt.0) zi=zi+boxzsize
+c xi=xi+xshift*boxxsize
+c yi=yi+yshift*boxysize
+c zi=zi+zshift*boxzsize
+c print *,xi,yi,zi,'polozenie i'
+C Return atom into box, boxxsize is size of box in x dimension
+c 134 continue
+c if (xi.gt.((xshift+0.5d0)*boxxsize)) xi=xi-boxxsize
+c if (xi.lt.((xshift-0.5d0)*boxxsize)) xi=xi+boxxsize
+C Condition for being inside the proper box
+c if ((xi.gt.((xshift+0.5d0)*boxxsize)).or.
+c & (xi.lt.((xshift-0.5d0)*boxxsize))) then
+c go to 134
+c endif
+c 135 continue
+c print *,xi,boxxsize,"pierwszy"
+c if (yi.gt.((yshift+0.5d0)*boxysize)) yi=yi-boxysize
+c if (yi.lt.((yshift-0.5d0)*boxysize)) yi=yi+boxysize
+C Condition for being inside the proper box
+c if ((yi.gt.((yshift+0.5d0)*boxysize)).or.
+c & (yi.lt.((yshift-0.5d0)*boxysize))) then
+c go to 135
+c endif
+c 136 continue
+c if (zi.gt.((zshift+0.5d0)*boxzsize)) zi=zi-boxzsize
+c if (zi.lt.((zshift-0.5d0)*boxzsize)) zi=zi+boxzsize
+C Condition for being inside the proper box
+c if ((zi.gt.((zshift+0.5d0)*boxzsize)).or.
+c & (zi.lt.((zshift-0.5d0)*boxzsize))) then
+c go to 136
+c endif
do iint=1,nscp_gr(i)
do j=iscpstart(i,iint),iscpend(i,iint)
- itypj=itype(j)
- if (itypj.eq.21) cycle
+ itypj=iabs(itype(j))
+ if (itypj.eq.ntyp1) cycle
C Uncomment following three lines for SC-p interactions
c xj=c(1,nres+j)-xi
c yj=c(2,nres+j)-yi
c zj=c(3,nres+j)-zi
C Uncomment following three lines for Ca-p interactions
- xj=c(1,j)-xi
- yj=c(2,j)-yi
- zj=c(3,j)-zi
+ xj=c(1,j)
+ yj=c(2,j)
+ zj=c(3,j)
+ xj=mod(xj,boxxsize)
+ if (xj.lt.0) xj=xj+boxxsize
+ yj=mod(yj,boxysize)
+ if (yj.lt.0) yj=yj+boxysize
+ zj=mod(zj,boxzsize)
+ if (zj.lt.0) zj=zj+boxzsize
+c 174 continue
+c if (xj.gt.((0.5d0)*boxxsize)) xj=xj-boxxsize
+c if (xj.lt.((-0.5d0)*boxxsize)) xj=xj+boxxsize
+C Condition for being inside the proper box
+c if ((xj.gt.((0.5d0)*boxxsize)).or.
+c & (xj.lt.((-0.5d0)*boxxsize))) then
+c go to 174
+c endif
+c 175 continue
+c if (yj.gt.((0.5d0)*boxysize)) yj=yj-boxysize
+c if (yj.lt.((-0.5d0)*boxysize)) yj=yj+boxysize
+cC Condition for being inside the proper box
+c if ((yj.gt.((0.5d0)*boxysize)).or.
+c & (yj.lt.((-0.5d0)*boxysize))) then
+c go to 175
+c endif
+c 176 continue
+c if (zj.gt.((0.5d0)*boxzsize)) zj=zj-boxzsize
+c if (zj.lt.((-0.5d0)*boxzsize)) zj=zj+boxzsize
+C Condition for being inside the proper box
+c if ((zj.gt.((0.5d0)*boxzsize)).or.
+c & (zj.lt.((-0.5d0)*boxzsize))) then
+c go to 176
+c endif
+CHERE IS THE CALCULATION WHICH MIRROR IMAGE IS THE CLOSEST ONE
+ dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
+ xj_safe=xj
+ yj_safe=yj
+ zj_safe=zj
+ subchap=0
+ do xshift=-1,1
+ do yshift=-1,1
+ do zshift=-1,1
+ xj=xj_safe+xshift*boxxsize
+ yj=yj_safe+yshift*boxysize
+ zj=zj_safe+zshift*boxzsize
+ dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
+ if(dist_temp.lt.dist_init) then
+ dist_init=dist_temp
+ xj_temp=xj
+ yj_temp=yj
+ zj_temp=zj
+ subchap=1
+ endif
+ enddo
+ enddo
+ enddo
+ if (subchap.eq.1) then
+ xj=xj_temp-xi
+ yj=yj_temp-yi
+ zj=zj_temp-zi
+ else
+ xj=xj_safe-xi
+ yj=yj_safe-yi
+ zj=zj_safe-zi
+ endif
+c print *,xj,yj,zj,'polozenie j'
rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
+c print *,rrij
+ sss=sscale(1.0d0/(dsqrt(rrij)))
+c print *,r_cut,1.0d0/dsqrt(rrij),sss,'tu patrz'
+c if (sss.eq.0) print *,'czasem jest OK'
+ if (sss.le.0.0d0) cycle
+ sssgrad=sscagrad(1.0d0/(dsqrt(rrij)))
fac=rrij**expon2
e1=fac*fac*aad(itypj,iteli)
e2=fac*bad(itypj,iteli)
if (iabs(j-i) .le. 2) then
e1=scal14*e1
e2=scal14*e2
- evdw2_14=evdw2_14+e1+e2
+ evdw2_14=evdw2_14+(e1+e2)*sss
endif
evdwij=e1+e2
- evdw2=evdw2+evdwij
- if (energy_dec) write (iout,'(a6,2i5,0pf7.3)')
- & 'evdw2',i,j,evdwij
+ evdw2=evdw2+evdwij*sss
+ if (energy_dec) write (iout,'(a6,2i5,0pf7.3,2i3,3e11.3)')
+ & 'evdw2',i,j,evdwij,iteli,itypj,fac,aad(itypj,iteli),
+ & bad(itypj,iteli)
C
C Calculate contributions to the gradient in the virtual-bond and SC vectors.
C
- fac=-(evdwij+e1)*rrij
+ fac=-(evdwij+e1)*rrij*sss
+ fac=fac+(evdwij)*sssgrad*dsqrt(rrij)/expon
ggg(1)=xj*fac
ggg(2)=yj*fac
ggg(3)=zj*fac
gvdwc_scpp(k,i)=gvdwc_scpp(k,i)-ggg(k)
gvdwc_scp(k,j)=gvdwc_scp(k,j)+ggg(k)
enddo
- enddo
+c endif !endif for sscale cutoff
+ enddo ! j
enddo ! iint
enddo ! i
+c enddo !zshift
+c enddo !yshift
+c enddo !xshift
do i=1,nct
do j=1,3
gvdwc_scp(j,i)=expon*gvdwc_scp(j,i)
C use!
C
C******************************************************************************
+c write (iout,*) "gvdwc_scp"
+c do i=1,nres
+c write (iout,'(i5,3f10.5,5x,3f10.5)') i,(gvdwc_scp(j,i),j=1,3),
+c & (gvdwc_scpp(j,i),j=1,3)
+c enddo
+
return
end
C--------------------------------------------------------------------------
include 'COMMON.VAR'
include 'COMMON.INTERACT'
include 'COMMON.IOUNITS'
+ include 'COMMON.CONTROL'
dimension ggg(3)
ehpb=0.0D0
+ do i=1,3
+ ggg(i)=0.0d0
+ enddo
+C write (iout,*) ,"link_end",link_end,constr_dist
cd write(iout,*)'edis: nhpb=',nhpb,' fbr=',fbr
cd write(iout,*)'link_start=',link_start,' link_end=',link_end
if (link_end.eq.0) return
iii=ii
jjj=jj
endif
-cd write (iout,*) "i",i," ii",ii," iii",iii," jj",jj," jjj",jjj
+c write (iout,*) "i",i," ii",ii," iii",iii," jj",jj," jjj",jjj,
+c & dhpb(i),dhpb1(i),forcon(i)
C 24/11/03 AL: SS bridges handled separately because of introducing a specific
C distance and angle dependent SS bond potential.
- if (ii.gt.nres .and. itype(iii).eq.1 .and. itype(jjj).eq.1) then
+C if (ii.gt.nres .and. iabs(itype(iii)).eq.1 .and.
+C & iabs(itype(jjj)).eq.1) then
+cmc if (ii.gt.nres .and. itype(iii).eq.1 .and. itype(jjj).eq.1) then
+C 18/07/06 MC: Use the convention that the first nss pairs are SS bonds
+ if (.not.dyn_ss .and. i.le.nss) then
+C 15/02/13 CC dynamic SSbond - additional check
+ if (ii.gt.nres .and. iabs(itype(iii)).eq.1 .and.
+ & iabs(itype(jjj)).eq.1) then
call ssbond_ene(iii,jjj,eij)
ehpb=ehpb+2*eij
+ endif
cd write (iout,*) "eij",eij
+cd & ' waga=',waga,' fac=',fac
+ else if (ii.gt.nres .and. jj.gt.nres) then
+c Restraints from contact prediction
+ dd=dist(ii,jj)
+ if (constr_dist.eq.11) then
+ ehpb=ehpb+fordepth(i)!**4.0d0
+ & *rlornmr1(dd,dhpb(i),dhpb1(i),forcon(i))
+ fac=fordepth(i)!**4.0d0
+ & *rlornmr1prim(dd,dhpb(i),dhpb1(i),forcon(i))/dd
+ if (energy_dec) write (iout,'(a6,2i5,6f10.3)') "edisl",ii,jj,
+ & dd,dhpb(i),dhpb1(i),forcon(i),fordepth(i),ehpb
+ else
+ if (dhpb1(i).gt.0.0d0) then
+ ehpb=ehpb+2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
+ fac=forcon(i)*gnmr1prim(dd,dhpb(i),dhpb1(i))/dd
+c write (iout,*) "beta nmr",
+c & dd,2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
+ else
+ dd=dist(ii,jj)
+ rdis=dd-dhpb(i)
+C Get the force constant corresponding to this distance.
+ waga=forcon(i)
+C Calculate the contribution to energy.
+ ehpb=ehpb+waga*rdis*rdis
+c write (iout,*) "beta reg",dd,waga*rdis*rdis
+C
+C Evaluate gradient.
+C
+ fac=waga*rdis/dd
+ endif
+ endif
+ do j=1,3
+ ggg(j)=fac*(c(j,jj)-c(j,ii))
+ enddo
+ do j=1,3
+ ghpbx(j,iii)=ghpbx(j,iii)-ggg(j)
+ ghpbx(j,jjj)=ghpbx(j,jjj)+ggg(j)
+ enddo
+ do k=1,3
+ ghpbc(k,jjj)=ghpbc(k,jjj)+ggg(k)
+ ghpbc(k,iii)=ghpbc(k,iii)-ggg(k)
+ enddo
else
C Calculate the distance between the two points and its difference from the
C target distance.
- dd=dist(ii,jj)
- rdis=dd-dhpb(i)
+ dd=dist(ii,jj)
+ if (constr_dist.eq.11) then
+ ehpb=ehpb+fordepth(i)!**4.0d0
+ & *rlornmr1(dd,dhpb(i),dhpb1(i),forcon(i))
+ fac=fordepth(i)!**4.0d0
+ & *rlornmr1prim(dd,dhpb(i),dhpb1(i),forcon(i))/dd
+ if (energy_dec) write (iout,'(a6,2i5,6f10.3)') "edisl",ii,jj,
+ & dd,dhpb(i),dhpb1(i),forcon(i),fordepth(i),ehpb
+ else
+ if (dhpb1(i).gt.0.0d0) then
+ ehpb=ehpb+2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
+ fac=forcon(i)*gnmr1prim(dd,dhpb(i),dhpb1(i))/dd
+c write (iout,*) "alph nmr",
+c & dd,2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
+ else
+ rdis=dd-dhpb(i)
C Get the force constant corresponding to this distance.
- waga=forcon(i)
+ waga=forcon(i)
C Calculate the contribution to energy.
- ehpb=ehpb+waga*rdis*rdis
+ ehpb=ehpb+waga*rdis*rdis
+c write (iout,*) "alpha reg",dd,waga*rdis*rdis
C
C Evaluate gradient.
C
- fac=waga*rdis/dd
-cd print *,'i=',i,' ii=',ii,' jj=',jj,' dhpb=',dhpb(i),' dd=',dd,
-cd & ' waga=',waga,' fac=',fac
- do j=1,3
- ggg(j)=fac*(c(j,jj)-c(j,ii))
- enddo
+ fac=waga*rdis/dd
+ endif
+ endif
+ do j=1,3
+ ggg(j)=fac*(c(j,jj)-c(j,ii))
+ enddo
cd print '(i3,3(1pe14.5))',i,(ggg(j),j=1,3)
C If this is a SC-SC distance, we need to calculate the contributions to the
C Cartesian gradient in the SC vectors (ghpbx).
- if (iii.lt.ii) then
+ if (iii.lt.ii) then
do j=1,3
ghpbx(j,iii)=ghpbx(j,iii)-ggg(j)
ghpbx(j,jjj)=ghpbx(j,jjj)+ggg(j)
enddo
- endif
+ endif
cgrad do j=iii,jjj-1
cgrad do k=1,3
cgrad ghpbc(k,j)=ghpbc(k,j)+ggg(k)
cgrad enddo
cgrad enddo
- do k=1,3
- ghpbc(k,jjj)=ghpbc(k,jjj)+ggg(k)
- ghpbc(k,iii)=ghpbc(k,iii)-ggg(k)
- enddo
+ do k=1,3
+ ghpbc(k,jjj)=ghpbc(k,jjj)+ggg(k)
+ ghpbc(k,iii)=ghpbc(k,iii)-ggg(k)
+ enddo
endif
enddo
- ehpb=0.5D0*ehpb
+ if (constr_dist.ne.11) ehpb=0.5D0*ehpb
return
end
C--------------------------------------------------------------------------
include 'COMMON.VAR'
include 'COMMON.IOUNITS'
double precision erij(3),dcosom1(3),dcosom2(3),gg(3)
- itypi=itype(i)
+ itypi=iabs(itype(i))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
dzi=dc_norm(3,nres+i)
c dsci_inv=dsc_inv(itypi)
dsci_inv=vbld_inv(nres+i)
- itypj=itype(j)
+ itypj=iabs(itype(j))
c dscj_inv=dsc_inv(itypj)
dscj_inv=vbld_inv(nres+j)
xj=c(1,nres+j)-xi
estr=0.0d0
estr1=0.0d0
do i=ibondp_start,ibondp_end
- if (itype(i-1).eq.21 .or. itype(i).eq.21) then
- estr1=estr1+gnmr1(vbld(i),-1.0d0,distchainmax)
- do j=1,3
- gradb(j,i-1)=gnmr1prim(vbld(i),-1.0d0,distchainmax)
- & *dc(j,i-1)/vbld(i)
- enddo
- if (energy_dec) write(iout,*)
- & "estr1",i,gnmr1(vbld(i),-1.0d0,distchainmax)
- else
+ if (itype(i-1).eq.ntyp1 .and. itype(i).eq.ntyp1) cycle
+c estr1=estr1+gnmr1(vbld(i),-1.0d0,distchainmax)
+c do j=1,3
+c gradb(j,i-1)=gnmr1prim(vbld(i),-1.0d0,distchainmax)
+c & *dc(j,i-1)/vbld(i)
+c enddo
+c if (energy_dec) write(iout,*)
+c & "estr1",i,gnmr1(vbld(i),-1.0d0,distchainmax)
+c else
+C Checking if it involves dummy (NH3+ or COO-) group
+ if (itype(i-1).eq.ntyp1 .or. itype(i).eq.ntyp1) then
+C YES vbldpDUM is the equlibrium length of spring for Dummy atom
+ diff = vbld(i)-vbldpDUM
+ 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
- if (energy_dec) write (iout,*)
+ endif
+ if (energy_dec) write (iout,'(a7,i5,4f7.3)')
& "estr bb",i,vbld(i),vbldp0,diff,AKP*diff*diff
estr=estr+diff*diff
do j=1,3
gradb(j,i-1)=AKP*diff*dc(j,i-1)/vbld(i)
enddo
c write (iout,'(i5,3f10.5)') i,(gradb(j,i-1),j=1,3)
- endif
+c endif
enddo
+
estr=0.5d0*AKP*estr+estr1
c
c 09/18/07 AL: multimodal bond potential based on AM1 CA-SC PMF's included
c
do i=ibond_start,ibond_end
- iti=itype(i)
- if (iti.ne.10 .and. iti.ne.21) then
+ iti=iabs(itype(i))
+ if (iti.ne.10 .and. iti.ne.ntyp1) then
nbi=nbondterm(iti)
if (nbi.eq.1) then
diff=vbld(i+nres)-vbldsc0(1,iti)
- if (energy_dec) write (iout,*)
+ if (energy_dec) write (iout,*)
& "estr sc",i,iti,vbld(i+nres),vbldsc0(1,iti),diff,
& AKSC(1,iti),AKSC(1,iti)*diff*diff
estr=estr+0.5d0*AKSC(1,iti)*diff*diff
include 'COMMON.NAMES'
include 'COMMON.FFIELD'
include 'COMMON.CONTROL'
+ include 'COMMON.TORCNSTR'
common /calcthet/ term1,term2,termm,diffak,ratak,
& ak,aktc,termpre,termexp,sigc,sig0i,time11,time12,sigcsq,
& delthe0,sig0inv,sigtc,sigsqtc,delthec,it
etheta=0.0D0
c write (*,'(a,i2)') 'EBEND ICG=',icg
do i=ithet_start,ithet_end
- if (itype(i-1).eq.21) cycle
+ if ((itype(i-1).eq.ntyp1).or.itype(i-2).eq.ntyp1
+ & .or.itype(i).eq.ntyp1) cycle
C Zero the energy function and its derivative at 0 or pi.
call splinthet(theta(i),0.5d0*delta,ss,ssd)
it=itype(i-1)
- if (i.gt.3 .and. itype(i-2).ne.21) then
+ ichir1=isign(1,itype(i-2))
+ ichir2=isign(1,itype(i))
+ if (itype(i-2).eq.10) ichir1=isign(1,itype(i-1))
+ if (itype(i).eq.10) ichir2=isign(1,itype(i-1))
+ if (itype(i-1).eq.10) then
+ itype1=isign(10,itype(i-2))
+ ichir11=isign(1,itype(i-2))
+ ichir12=isign(1,itype(i-2))
+ itype2=isign(10,itype(i))
+ ichir21=isign(1,itype(i))
+ ichir22=isign(1,itype(i))
+ endif
+
+ if (i.gt.3 .and. itype(i-3).ne.ntyp1) then
#ifdef OSF
phii=phi(i)
if (phii.ne.phii) phii=150.0
y(1)=0.0D0
y(2)=0.0D0
endif
- if (i.lt.nres .and. itype(i).ne.21) then
+ if (i.lt.nres .and. itype(i+1).ne.ntyp1) then
#ifdef OSF
phii1=phi(i+1)
if (phii1.ne.phii1) phii1=150.0
z(1)=cos(phii1)
#else
phii1=phi(i+1)
- z(1)=dcos(phii1)
#endif
+ z(1)=dcos(phii1)
z(2)=dsin(phii1)
else
z(1)=0.0D0
C In following comments this theta will be referred to as t_c.
thet_pred_mean=0.0d0
do k=1,2
- athetk=athet(k,it)
- bthetk=bthet(k,it)
- thet_pred_mean=thet_pred_mean+athetk*y(k)+bthetk*z(k)
+ athetk=athet(k,it,ichir1,ichir2)
+ bthetk=bthet(k,it,ichir1,ichir2)
+ if (it.eq.10) then
+ athetk=athet(k,itype1,ichir11,ichir12)
+ bthetk=bthet(k,itype2,ichir21,ichir22)
+ endif
+ thet_pred_mean=thet_pred_mean+athetk*y(k)+bthetk*z(k)
+c write(iout,*) 'chuj tu', y(k),z(k)
enddo
dthett=thet_pred_mean*ssd
thet_pred_mean=thet_pred_mean*ss+a0thet(it)
C Derivatives of the "mean" values in gamma1 and gamma2.
- dthetg1=(-athet(1,it)*y(2)+athet(2,it)*y(1))*ss
- dthetg2=(-bthet(1,it)*z(2)+bthet(2,it)*z(1))*ss
+ dthetg1=(-athet(1,it,ichir1,ichir2)*y(2)
+ &+athet(2,it,ichir1,ichir2)*y(1))*ss
+ dthetg2=(-bthet(1,it,ichir1,ichir2)*z(2)
+ & +bthet(2,it,ichir1,ichir2)*z(1))*ss
+ if (it.eq.10) then
+ dthetg1=(-athet(1,itype1,ichir11,ichir12)*y(2)
+ &+athet(2,itype1,ichir11,ichir12)*y(1))*ss
+ dthetg2=(-bthet(1,itype2,ichir21,ichir22)*z(2)
+ & +bthet(2,itype2,ichir21,ichir22)*z(1))*ss
+ endif
if (theta(i).gt.pi-delta) then
call theteng(pi-delta,thet_pred_mean,theta0(it),f0,fprim0,
& E_tc0)
& E_theta,E_tc)
endif
etheta=etheta+ethetai
- if (energy_dec) write (iout,'(a6,i5,0pf7.3)')
- & 'ebend',i,ethetai
+ if (energy_dec) write (iout,'(a6,i5,0pf7.3,f7.3,i5)')
+ & 'ebend',i,ethetai,theta(i),itype(i)
if (i.gt.3) gloc(i-3,icg)=gloc(i-3,icg)+wang*E_tc*dthetg1
if (i.lt.nres) gloc(i-2,icg)=gloc(i-2,icg)+wang*E_tc*dthetg2
- gloc(nphi+i-2,icg)=wang*(E_theta+E_tc*dthett)
+ gloc(nphi+i-2,icg)=wang*(E_theta+E_tc*dthett)+gloc(nphi+i-2,icg)
enddo
+
C Ufff.... We've done all this!!!
return
end
C Calculate the contributions to both Gaussian lobes.
C 6/6/97 - Deform the Gaussians using the factor of 1/(1+time)
C The "polynomial part" of the "standard deviation" of this part of
-C the distribution.
+C the distributioni.
+ccc write (iout,*) thetai,thet_pred_mean
sig=polthet(3,it)
do j=2,0,-1
sig=sig*thet_pred_mean+polthet(j,it)
delthe0=thetai-theta0i
term1=-0.5D0*sigcsq*delthec*delthec
term2=-0.5D0*sig0inv*delthe0*delthe0
+C write (iout,*)'term1',term1,term2,sigcsq,delthec,sig0inv,delthe0
C Following fuzzy logic is to avoid underflows in dexp and subsequent INFs and
C NaNs in taking the logarithm. We extract the largest exponent which is added
C to the energy (this being the log of the distribution) at the end of energy
C the sum of the contributions from the two lobes and the pre-exponential
C factor. Simple enough, isn't it?
ethetai=(-dlog(termexp)-termm+dlog(termpre))
+C write (iout,*) 'termexp',termexp,termm,termpre,i
C NOW the derivatives!!!
C 6/6/97 Take into account the deformation.
E_theta=(delthec*sigcsq*term1
include 'COMMON.NAMES'
include 'COMMON.FFIELD'
include 'COMMON.CONTROL'
+ include 'COMMON.TORCNSTR'
double precision coskt(mmaxtheterm),sinkt(mmaxtheterm),
& cosph1(maxsingle),sinph1(maxsingle),cosph2(maxsingle),
& sinph2(maxsingle),cosph1ph2(maxdouble,maxdouble),
logical lprn /.false./, lprn1 /.false./
etheta=0.0D0
do i=ithet_start,ithet_end
- if (itype(i-1).eq.21) cycle
+c print *,i,itype(i-1),itype(i),itype(i-2)
+ if ((itype(i-1).eq.ntyp1).or.itype(i-2).eq.ntyp1
+ & .or.itype(i).eq.ntyp1) cycle
+C print *,i,theta(i)
+ if (iabs(itype(i+1)).eq.20) iblock=2
+ if (iabs(itype(i+1)).ne.20) iblock=1
dethetai=0.0d0
dephii=0.0d0
dephii1=0.0d0
theti2=0.5d0*theta(i)
- ityp2=ithetyp(itype(i-1))
+ ityp2=ithetyp((itype(i-1)))
do k=1,nntheterm
coskt(k)=dcos(k*theti2)
sinkt(k)=dsin(k*theti2)
enddo
- if (i.gt.3 .and. itype(i-2).ne.21) then
+C print *,ethetai
+ if (i.gt.3 .and. itype(i-3).ne.ntyp1) then
#ifdef OSF
phii=phi(i)
if (phii.ne.phii) phii=150.0
#else
phii=phi(i)
#endif
- ityp1=ithetyp(itype(i-2))
+ ityp1=ithetyp((itype(i-2)))
+C propagation of chirality for glycine type
do k=1,nsingle
cosph1(k)=dcos(k*phii)
sinph1(k)=dsin(k*phii)
enddo
else
phii=0.0d0
- ityp1=nthetyp+1
do k=1,nsingle
+ ityp1=ithetyp((itype(i-2)))
cosph1(k)=0.0d0
sinph1(k)=0.0d0
enddo
endif
- if (i.lt.nres .and. itype(i).ne.21) then
+ if (i.lt.nres .and. itype(i+1).ne.ntyp1) then
#ifdef OSF
phii1=phi(i+1)
if (phii1.ne.phii1) phii1=150.0
#else
phii1=phi(i+1)
#endif
- ityp3=ithetyp(itype(i))
+ ityp3=ithetyp((itype(i)))
do k=1,nsingle
cosph2(k)=dcos(k*phii1)
sinph2(k)=dsin(k*phii1)
enddo
else
phii1=0.0d0
- ityp3=nthetyp+1
+ ityp3=ithetyp((itype(i)))
do k=1,nsingle
cosph2(k)=0.0d0
sinph2(k)=0.0d0
enddo
endif
- ethetai=aa0thet(ityp1,ityp2,ityp3)
+ ethetai=aa0thet(ityp1,ityp2,ityp3,iblock)
do k=1,ndouble
do l=1,k-1
ccl=cosph1(l)*cosph2(k-l)
enddo
endif
do k=1,ntheterm
- ethetai=ethetai+aathet(k,ityp1,ityp2,ityp3)*sinkt(k)
- dethetai=dethetai+0.5d0*k*aathet(k,ityp1,ityp2,ityp3)
+ ethetai=ethetai+aathet(k,ityp1,ityp2,ityp3,iblock)*sinkt(k)
+ dethetai=dethetai+0.5d0*k*aathet(k,ityp1,ityp2,ityp3,iblock)
& *coskt(k)
if (lprn)
- & write (iout,*) "k",k," aathet",aathet(k,ityp1,ityp2,ityp3),
+ & write (iout,*) "k",k,"
+ & aathet",aathet(k,ityp1,ityp2,ityp3,iblock),
& " ethetai",ethetai
enddo
if (lprn) then
enddo
write(iout,*) "ethetai",ethetai
endif
+C print *,ethetai
do m=1,ntheterm2
do k=1,nsingle
- aux=bbthet(k,m,ityp1,ityp2,ityp3)*cosph1(k)
- & +ccthet(k,m,ityp1,ityp2,ityp3)*sinph1(k)
- & +ddthet(k,m,ityp1,ityp2,ityp3)*cosph2(k)
- & +eethet(k,m,ityp1,ityp2,ityp3)*sinph2(k)
+ aux=bbthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph1(k)
+ & +ccthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph1(k)
+ & +ddthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph2(k)
+ & +eethet(k,m,ityp1,ityp2,ityp3,iblock)*sinph2(k)
ethetai=ethetai+sinkt(m)*aux
dethetai=dethetai+0.5d0*m*aux*coskt(m)
dephii=dephii+k*sinkt(m)*(
- & ccthet(k,m,ityp1,ityp2,ityp3)*cosph1(k)-
- & bbthet(k,m,ityp1,ityp2,ityp3)*sinph1(k))
+ & ccthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph1(k)-
+ & bbthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph1(k))
dephii1=dephii1+k*sinkt(m)*(
- & eethet(k,m,ityp1,ityp2,ityp3)*cosph2(k)-
- & ddthet(k,m,ityp1,ityp2,ityp3)*sinph2(k))
+ & eethet(k,m,ityp1,ityp2,ityp3,iblock)*cosph2(k)-
+ & ddthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph2(k))
if (lprn)
& write (iout,*) "m",m," k",k," bbthet",
- & bbthet(k,m,ityp1,ityp2,ityp3)," ccthet",
- & ccthet(k,m,ityp1,ityp2,ityp3)," ddthet",
- & ddthet(k,m,ityp1,ityp2,ityp3)," eethet",
- & eethet(k,m,ityp1,ityp2,ityp3)," ethetai",ethetai
+ & bbthet(k,m,ityp1,ityp2,ityp3,iblock)," ccthet",
+ & ccthet(k,m,ityp1,ityp2,ityp3,iblock)," ddthet",
+ & ddthet(k,m,ityp1,ityp2,ityp3,iblock)," eethet",
+ & eethet(k,m,ityp1,ityp2,ityp3,iblock)," ethetai",ethetai
+C print *,"tu",cosph1(k),sinph1(k),cosph2(k),sinph2(k)
enddo
enddo
+C print *,"cosph1", (cosph1(k), k=1,nsingle)
+C print *,"cosph2", (cosph2(k), k=1,nsingle)
+C print *,"sinph1", (sinph1(k), k=1,nsingle)
+C print *,"sinph2", (sinph2(k), k=1,nsingle)
if (lprn)
& write(iout,*) "ethetai",ethetai
+C print *,"tu",cosph1(k),sinph1(k),cosph2(k),sinph2(k)
do m=1,ntheterm3
do k=2,ndouble
do l=1,k-1
- aux=ffthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)+
- & ffthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l)+
- & ggthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)+
- & ggthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)
+ aux=ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)+
+ & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l)+
+ & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)+
+ & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l)
ethetai=ethetai+sinkt(m)*aux
dethetai=dethetai+0.5d0*m*coskt(m)*aux
dephii=dephii+l*sinkt(m)*(
- & -ffthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)-
- & ffthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)+
- & ggthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)+
- & ggthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l))
+ & -ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)-
+ & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l)+
+ & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)+
+ & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l))
dephii1=dephii1+(k-l)*sinkt(m)*(
- & -ffthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)+
- & ffthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)+
- & ggthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)-
- & ggthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l))
+ & -ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)+
+ & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l)+
+ & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)-
+ & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l))
if (lprn) then
write (iout,*) "m",m," k",k," l",l," ffthet",
- & ffthet(l,k,m,ityp1,ityp2,ityp3),
- & ffthet(k,l,m,ityp1,ityp2,ityp3)," ggthet",
- & ggthet(l,k,m,ityp1,ityp2,ityp3),
- & ggthet(k,l,m,ityp1,ityp2,ityp3)," ethetai",ethetai
+ & ffthet(l,k,m,ityp1,ityp2,ityp3,iblock),
+ & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)," ggthet",
+ & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock),
+ & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock),
+ & " ethetai",ethetai
write (iout,*) cosph1ph2(l,k)*sinkt(m),
& cosph1ph2(k,l)*sinkt(m),
& sinph1ph2(l,k)*sinkt(m),sinph1ph2(k,l)*sinkt(m)
enddo
enddo
10 continue
- if (lprn1) write (iout,'(i2,3f8.1,9h ethetai ,f10.5)')
+c lprn1=.true.
+C print *,ethetai
+ if (lprn1)
+ & write (iout,'(i2,3f8.1,9h ethetai ,f10.5)')
& i,theta(i)*rad2deg,phii*rad2deg,
& phii1*rad2deg,ethetai
+c lprn1=.false.
etheta=etheta+ethetai
if (i.gt.3) gloc(i-3,icg)=gloc(i-3,icg)+wang*dephii
if (i.lt.nres) gloc(i-2,icg)=gloc(i-2,icg)+wang*dephii1
- gloc(nphi+i-2,icg)=wang*dethetai
+ gloc(nphi+i-2,icg)=gloc(nphi+i-2,icg)+wang*dethetai
enddo
+
return
end
#endif
c write (iout,'(a)') 'ESC'
do i=loc_start,loc_end
it=itype(i)
- if (it.eq.21) cycle
+ if (it.eq.ntyp1) cycle
if (it.eq.10) goto 1
- nlobit=nlob(it)
+ nlobit=nlob(iabs(it))
c print *,'i=',i,' it=',it,' nlobit=',nlobit
c write (iout,*) 'i=',i,' ssa=',ssa,' ssad=',ssad
theti=theta(i+1)-pipol
do j=1,nlobit
#ifdef OSF
- adexp=bsc(j,it)-0.5D0*contr(j,iii)+emin
+ adexp=bsc(j,iabs(it))-0.5D0*contr(j,iii)+emin
if(adexp.ne.adexp) adexp=1.0
expfac=dexp(adexp)
#else
- expfac=dexp(bsc(j,it)-0.5D0*contr(j,iii)+emin)
+ expfac=dexp(bsc(j,iabs(it))-0.5D0*contr(j,iii)+emin)
#endif
cd print *,'j=',j,' expfac=',expfac
escloc_i=escloc_i+expfac
dersc12=0.0d0
do j=1,nlobit
- expfac=dexp(bsc(j,it)-0.5D0*contr(j)+emin)
+ expfac=dexp(bsc(j,iabs(it))-0.5D0*contr(j)+emin)
escloc_i=escloc_i+expfac
do k=1,2
dersc(k)=dersc(k)+Ax(k,j)*expfac
delta=0.02d0*pi
escloc=0.0D0
do i=loc_start,loc_end
- if (itype(i).eq.21) cycle
+ if (itype(i).eq.ntyp1) cycle
costtab(i+1) =dcos(theta(i+1))
sinttab(i+1) =dsqrt(1-costtab(i+1)*costtab(i+1))
cost2tab(i+1)=dsqrt(0.5d0*(1.0d0+costtab(i+1)))
cosfac=dsqrt(cosfac2)
sinfac2=0.5d0/(1.0d0-costtab(i+1))
sinfac=dsqrt(sinfac2)
- it=itype(i)
+ it=iabs(itype(i))
if (it.eq.10) goto 1
c
C Compute the axes of tghe local cartesian coordinates system; store in
y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac
enddo
do j = 1,3
- z_prime(j) = -uz(j,i-1)
+ z_prime(j) = -uz(j,i-1)*dsign(1.0d0,dfloat(itype(i)))
enddo
c write (2,*) "i",i
c write (2,*) "x_prime",(x_prime(j),j=1,3)
C Compute the energy of the ith side cbain
C
c write (2,*) "xx",xx," yy",yy," zz",zz
- it=itype(i)
+ it=iabs(itype(i))
do j = 1,65
x(j) = sc_parmin(j,it)
enddo
Cc diagnostics - remove later
xx1 = dcos(alph(2))
yy1 = dsin(alph(2))*dcos(omeg(2))
- zz1 = -dsin(alph(2))*dsin(omeg(2))
+ zz1 = -dsign(1.0,dfloat(itype(i)))*dsin(alph(2))*dsin(omeg(2))
write(2,'(3f8.1,3f9.3,1x,3f9.3)')
& alph(2)*rad2deg,omeg(2)*rad2deg,theta(3)*rad2deg,xx,yy,zz,
& xx1,yy1,zz1
c & dscp1,dscp2,sumene
c sumene = enesc(x,xx,yy,zz,cost2tab(i+1),sint2tab(i+1))
escloc = escloc + sumene
-c write (2,*) "i",i," escloc",sumene,escloc
+c write (2,*) "i",i," escloc",sumene,escloc,it,itype(i)
+c & ,zz,xx,yy
+c#define DEBUG
#ifdef DEBUG
C
C This section to check the numerical derivatives of the energy of ith side
C
C Compute the gradient of esc
C
+c zz=zz*dsign(1.0,dfloat(itype(i)))
pom_s1=(1.0d0+x(63))/(0.1d0 + dscp1)**2
pom_s16=6*(1.0d0+x(64))/(0.1d0 + dscp1**6)**2
pom_s2=(1.0d0+x(65))/(0.1d0 + dscp2)**2
& +(sumene2x+sumene4x*cost2tab(i+1))*(s2+s2_6)
& +(pom1+pom2)*pom_dx
#ifdef DEBUG
- write(2,*), "de_dxx = ", de_dxx,de_dxx_num
+ write(2,*), "de_dxx = ", de_dxx,de_dxx_num,itype(i)
#endif
C
sumene1y=x(3) + 2*x(6)*yy + x(9)*xx + x(10)*zz
& +(sumene2y+sumene4y*cost2tab(i+1))*(s2+s2_6)
& +(pom1-pom2)*pom_dy
#ifdef DEBUG
- write(2,*), "de_dyy = ", de_dyy,de_dyy_num
+ write(2,*), "de_dyy = ", de_dyy,de_dyy_num,itype(i)
#endif
C
de_dzz =(x(24) +2*x(27)*zz +x(28)*xx +x(30)*yy
& +x(60)*xx*yy)*cost2tab(i+1)*(s2+s2_6)
& + ( x(14) + 2*x(17)*zz+ x(18)*xx + x(20)*yy)*(s2+s2_6)
#ifdef DEBUG
- write(2,*), "de_dzz = ", de_dzz,de_dzz_num
+ write(2,*), "de_dzz = ", de_dzz,de_dzz_num,itype(i)
#endif
C
de_dt = 0.5d0*sumene3*cost2tab(i+1)*(s1+s1_6)
& -0.5d0*sumene4*sint2tab(i+1)*(s2+s2_6)
& +pom1*pom_dt1+pom2*pom_dt2
#ifdef DEBUG
- write(2,*), "de_dt = ", de_dt,de_dt_num
+ write(2,*), "de_dt = ", de_dt,de_dt_num,itype(i)
#endif
+c#undef DEBUG
c
C
cossc=scalar(dc_norm(1,i),dc_norm(1,i+nres))
dZZ_Ci1(k)=0.0d0
dZZ_Ci(k)=0.0d0
do j=1,3
- dZZ_Ci(k)=dZZ_Ci(k)-uzgrad(j,k,2,i-1)*dC_norm(j,i+nres)
- dZZ_Ci1(k)=dZZ_Ci1(k)-uzgrad(j,k,1,i-1)*dC_norm(j,i+nres)
+ dZZ_Ci(k)=dZZ_Ci(k)-uzgrad(j,k,2,i-1)
+ & *dsign(1.0d0,dfloat(itype(i)))*dC_norm(j,i+nres)
+ dZZ_Ci1(k)=dZZ_Ci1(k)-uzgrad(j,k,1,i-1)
+ & *dsign(1.0d0,dfloat(itype(i)))*dC_norm(j,i+nres)
enddo
dXX_XYZ(k)=vbld_inv(i+nres)*(x_prime(k)-xx*dC_norm(k,i+nres))
dYY_XYZ(k)=vbld_inv(i+nres)*(y_prime(k)-yy*dC_norm(k,i+nres))
- dZZ_XYZ(k)=vbld_inv(i+nres)*(z_prime(k)-zz*dC_norm(k,i+nres))
+ dZZ_XYZ(k)=vbld_inv(i+nres)*
+ & (z_prime(k)-zz*dC_norm(k,i+nres))
c
dt_dCi(k) = -dt_dCi(k)/sinttab(i+1)
dt_dCi1(k)= -dt_dCi1(k)/sinttab(i+1)
C-----------------------------------------------------------------------------
#ifdef CRYST_TOR
C-----------------------------------------------------------------------------
- subroutine etor(etors,edihcnstr)
+ subroutine etor(etors)
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
include 'COMMON.VAR'
etors=0.0D0
do i=iphi_start,iphi_end
etors_ii=0.0D0
- if (itype(i-2).eq.21 .or. itype(i-1).eq.21
- & .or. itype(i).eq.21) cycle
- itori=itortyp(itype(i-2))
- itori1=itortyp(itype(i-1))
+ if (itype(i-2).eq.ntyp1.or. itype(i-1).eq.ntyp1
+ & .or. itype(i).eq.ntyp1 .or. itype(i-3).eq.ntyp1) cycle
+ itori=itortyp(itype(i-2))
+ itori1=itortyp(itype(i-1))
phii=phi(i)
gloci=0.0D0
C Proline-Proline pair is a special case...
gloc(i-3,icg)=gloc(i-3,icg)+wtor*gloci
c write (iout,*) 'i=',i,' gloc=',gloc(i-3,icg)
enddo
-! 6/20/98 - dihedral angle constraints
- edihcnstr=0.0d0
- do i=1,ndih_constr
- itori=idih_constr(i)
- phii=phi(itori)
- difi=phii-phi0(i)
- if (difi.gt.drange(i)) then
- difi=difi-drange(i)
- edihcnstr=edihcnstr+0.25d0*ftors*difi**4
- gloc(itori-3,icg)=gloc(itori-3,icg)+ftors*difi**3
- else if (difi.lt.-drange(i)) then
- difi=difi+drange(i)
- edihcnstr=edihcnstr+0.25d0*ftors*difi**4
- gloc(itori-3,icg)=gloc(itori-3,icg)+ftors*difi**3
- endif
-! write (iout,'(2i5,2f8.3,2e14.5)') i,itori,rad2deg*phii,
-! & rad2deg*difi,0.25d0*ftors*difi**4,gloc(itori-3,icg)
- enddo
-! write (iout,*) 'edihcnstr',edihcnstr
return
end
c------------------------------------------------------------------------------
end
c----------------------------------------------------------------------------
#else
- subroutine etor(etors,edihcnstr)
+ subroutine etor(etors)
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
include 'COMMON.VAR'
c lprn=.true.
etors=0.0D0
do i=iphi_start,iphi_end
- if (itype(i-2).eq.21 .or. itype(i-1).eq.21
- & .or. itype(i).eq.21) cycle
+C ANY TWO ARE DUMMY ATOMS in row CYCLE
+c if (((itype(i-3).eq.ntyp1).and.(itype(i-2).eq.ntyp1)).or.
+c & ((itype(i-2).eq.ntyp1).and.(itype(i-1).eq.ntyp1)) .or.
+c & ((itype(i-1).eq.ntyp1).and.(itype(i).eq.ntyp1))) cycle
+ if (itype(i-2).eq.ntyp1.or. itype(i-1).eq.ntyp1
+ & .or. itype(i).eq.ntyp1 .or. itype(i-3).eq.ntyp1) cycle
+C In current verion the ALL DUMMY ATOM POTENTIALS ARE OFF
+C For introducing the NH3+ and COO- group please check the etor_d for reference
+C and guidance
etors_ii=0.0D0
+ if (iabs(itype(i)).eq.20) then
+ iblock=2
+ else
+ iblock=1
+ endif
itori=itortyp(itype(i-2))
itori1=itortyp(itype(i-1))
phii=phi(i)
gloci=0.0D0
C Regular cosine and sine terms
- do j=1,nterm(itori,itori1)
- v1ij=v1(j,itori,itori1)
- v2ij=v2(j,itori,itori1)
+ do j=1,nterm(itori,itori1,iblock)
+ v1ij=v1(j,itori,itori1,iblock)
+ v2ij=v2(j,itori,itori1,iblock)
cosphi=dcos(j*phii)
sinphi=dsin(j*phii)
etors=etors+v1ij*cosphi+v2ij*sinphi
C
cosphi=dcos(0.5d0*phii)
sinphi=dsin(0.5d0*phii)
- do j=1,nlor(itori,itori1)
+ do j=1,nlor(itori,itori1,iblock)
vl1ij=vlor1(j,itori,itori1)
vl2ij=vlor2(j,itori,itori1)
vl3ij=vlor3(j,itori,itori1)
gloci=gloci+vl1ij*(vl3ij*cosphi-vl2ij*sinphi)*pom
enddo
C Subtract the constant term
- etors=etors-v0(itori,itori1)
+ etors=etors-v0(itori,itori1,iblock)
if (energy_dec) write (iout,'(a6,i5,0pf7.3)')
- & 'etor',i,etors_ii-v0(itori,itori1)
+ & 'etor',i,etors_ii-v0(itori,itori1,iblock)
if (lprn)
& write (iout,'(2(a3,2x,i3,2x),2i3,6f8.3/26x,6f8.3/)')
& restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,itori,itori1,
- & (v1(j,itori,itori1),j=1,6),(v2(j,itori,itori1),j=1,6)
+ & (v1(j,itori,itori1,iblock),j=1,6),
+ & (v2(j,itori,itori1,iblock),j=1,6)
gloc(i-3,icg)=gloc(i-3,icg)+wtor*gloci
c write (iout,*) 'i=',i,' gloc=',gloc(i-3,icg)
enddo
-! 6/20/98 - dihedral angle constraints
- 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*difi**4
- gloc(itori-3,icg)=gloc(itori-3,icg)+ftors*difi**3
- else if (difi.lt.-drange(i)) then
- difi=difi+drange(i)
- edihcnstr=edihcnstr+0.25d0*ftors*difi**4
- gloc(itori-3,icg)=gloc(itori-3,icg)+ftors*difi**3
- else
- difi=0.0
- endif
-cd write (iout,'(2i5,4f8.3,2e14.5)') i,itori,rad2deg*phii,
-cd & rad2deg*phi0(i), rad2deg*drange(i),
-cd & rad2deg*difi,0.25d0*ftors*difi**4,gloc(itori-3,icg)
- enddo
-cd write (iout,*) 'edihcnstr',edihcnstr
return
end
c----------------------------------------------------------------------------
lprn=.false.
c lprn=.true.
etors_d=0.0D0
+c write(iout,*) "a tu??"
do i=iphid_start,iphid_end
- if (itype(i-2).eq.21 .or. itype(i-1).eq.21
- & .or. itype(i).eq.21 .or. itype(i+1).eq.21) cycle
+C ANY TWO ARE DUMMY ATOMS in row CYCLE
+C if (((itype(i-3).eq.ntyp1).and.(itype(i-2).eq.ntyp1)).or.
+C & ((itype(i-2).eq.ntyp1).and.(itype(i-1).eq.ntyp1)).or.
+C & ((itype(i-1).eq.ntyp1).and.(itype(i).eq.ntyp1)) .or.
+C & ((itype(i).eq.ntyp1).and.(itype(i+1).eq.ntyp1))) cycle
+ if ((itype(i-2).eq.ntyp1).or.itype(i-3).eq.ntyp1.or.
+ & (itype(i-1).eq.ntyp1).or.(itype(i).eq.ntyp1).or.
+ & (itype(i+1).eq.ntyp1)) cycle
+C In current verion the ALL DUMMY ATOM POTENTIALS ARE OFF
itori=itortyp(itype(i-2))
itori1=itortyp(itype(i-1))
itori2=itortyp(itype(i))
phii1=phi(i+1)
gloci1=0.0D0
gloci2=0.0D0
+ iblock=1
+ if (iabs(itype(i+1)).eq.20) iblock=2
+C Iblock=2 Proline type
+C ADASKO: WHEN PARAMETERS FOR THIS TYPE OF BLOCKING GROUP IS READY UNCOMMENT
+C CHECK WEATHER THERE IS NECCESITY FOR iblock=3 for COO-
+C if (itype(i+1).eq.ntyp1) iblock=3
+C The problem of NH3+ group can be resolved by adding new parameters please note if there
+C IS or IS NOT need for this
+C IF Yes uncomment below and add to parmread.F appropriate changes and to v1cij and so on
+C is (itype(i-3).eq.ntyp1) ntblock=2
+C ntblock is N-terminal blocking group
+
C Regular cosine and sine terms
- do j=1,ntermd_1(itori,itori1,itori2)
- v1cij=v1c(1,j,itori,itori1,itori2)
- v1sij=v1s(1,j,itori,itori1,itori2)
- v2cij=v1c(2,j,itori,itori1,itori2)
- v2sij=v1s(2,j,itori,itori1,itori2)
+ do j=1,ntermd_1(itori,itori1,itori2,iblock)
+C Example of changes for NH3+ blocking group
+C do j=1,ntermd_1(itori,itori1,itori2,iblock,ntblock)
+C v1cij=v1c(1,j,itori,itori1,itori2,iblock,ntblock)
+ v1cij=v1c(1,j,itori,itori1,itori2,iblock)
+ v1sij=v1s(1,j,itori,itori1,itori2,iblock)
+ v2cij=v1c(2,j,itori,itori1,itori2,iblock)
+ v2sij=v1s(2,j,itori,itori1,itori2,iblock)
cosphi1=dcos(j*phii)
sinphi1=dsin(j*phii)
cosphi2=dcos(j*phii1)
gloci1=gloci1+j*(v1sij*cosphi1-v1cij*sinphi1)
gloci2=gloci2+j*(v2sij*cosphi2-v2cij*sinphi2)
enddo
- do k=2,ntermd_2(itori,itori1,itori2)
+ do k=2,ntermd_2(itori,itori1,itori2,iblock)
do l=1,k-1
- v1cdij = v2c(k,l,itori,itori1,itori2)
- v2cdij = v2c(l,k,itori,itori1,itori2)
- v1sdij = v2s(k,l,itori,itori1,itori2)
- v2sdij = v2s(l,k,itori,itori1,itori2)
+ v1cdij = v2c(k,l,itori,itori1,itori2,iblock)
+ v2cdij = v2c(l,k,itori,itori1,itori2,iblock)
+ v1sdij = v2s(k,l,itori,itori1,itori2,iblock)
+ v2sdij = v2s(l,k,itori,itori1,itori2,iblock)
cosphi1p2=dcos(l*phii+(k-l)*phii1)
cosphi1m2=dcos(l*phii-(k-l)*phii1)
sinphi1p2=dsin(l*phii+(k-l)*phii1)
return
end
#endif
+C----------------------------------------------------------------------------------
+C The rigorous attempt to derive energy function
+ subroutine etor_kcc(etors)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.VAR'
+ include 'COMMON.GEO'
+ include 'COMMON.LOCAL'
+ include 'COMMON.TORSION'
+ include 'COMMON.INTERACT'
+ include 'COMMON.DERIV'
+ include 'COMMON.CHAIN'
+ include 'COMMON.NAMES'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.FFIELD'
+ include 'COMMON.TORCNSTR'
+ include 'COMMON.CONTROL'
+ double precision c1(0:maxval_kcc),c2(0:maxval_kcc)
+ logical lprn
+c double precision thybt1(maxtermkcc),thybt2(maxtermkcc)
+C Set lprn=.true. for debugging
+ lprn=energy_dec
+c lprn=.true.
+C print *,"wchodze kcc"
+ if (lprn) write (iout,*) "etor_kcc tor_mode",tor_mode
+ etors=0.0D0
+ do i=iphi_start,iphi_end
+C ANY TWO ARE DUMMY ATOMS in row CYCLE
+c if (((itype(i-3).eq.ntyp1).and.(itype(i-2).eq.ntyp1)).or.
+c & ((itype(i-2).eq.ntyp1).and.(itype(i-1).eq.ntyp1)) .or.
+c & ((itype(i-1).eq.ntyp1).and.(itype(i).eq.ntyp1))) cycle
+ if (itype(i-2).eq.ntyp1.or. itype(i-1).eq.ntyp1
+ & .or. itype(i).eq.ntyp1 .or. itype(i-3).eq.ntyp1) cycle
+ itori=itortyp(itype(i-2))
+ itori1=itortyp(itype(i-1))
+ phii=phi(i)
+ glocig=0.0D0
+ glocit1=0.0d0
+ glocit2=0.0d0
+C to avoid multiple devision by 2
+c theti22=0.5d0*theta(i)
+C theta 12 is the theta_1 /2
+C theta 22 is theta_2 /2
+c theti12=0.5d0*theta(i-1)
+C and appropriate sinus function
+ sinthet1=dsin(theta(i-1))
+ sinthet2=dsin(theta(i))
+ costhet1=dcos(theta(i-1))
+ costhet2=dcos(theta(i))
+C to speed up lets store its mutliplication
+ sint1t2=sinthet2*sinthet1
+ sint1t2n=1.0d0
+C \sum_{i=1}^n (sin(theta_1) * sin(theta_2))^n * (c_n* cos(n*gamma)
+C +d_n*sin(n*gamma)) *
+C \sum_{i=1}^m (1+a_m*Tb_m(cos(theta_1 /2))+b_m*Tb_m(cos(theta_2 /2)))
+C we have two sum 1) Non-Chebyshev which is with n and gamma
+ nval=nterm_kcc_Tb(itori,itori1)
+ c1(0)=0.0d0
+ c2(0)=0.0d0
+ c1(1)=1.0d0
+ c2(1)=1.0d0
+ do j=2,nval
+ c1(j)=c1(j-1)*costhet1
+ c2(j)=c2(j-1)*costhet2
+ enddo
+ etori=0.0d0
+ do j=1,nterm_kcc(itori,itori1)
+ cosphi=dcos(j*phii)
+ sinphi=dsin(j*phii)
+ sint1t2n1=sint1t2n
+ sint1t2n=sint1t2n*sint1t2
+ sumvalc=0.0d0
+ gradvalct1=0.0d0
+ gradvalct2=0.0d0
+ do k=1,nval
+ do l=1,nval
+ sumvalc=sumvalc+v1_kcc(l,k,j,itori1,itori)*c1(k)*c2(l)
+ gradvalct1=gradvalct1+
+ & (k-1)*v1_kcc(l,k,j,itori1,itori)*c1(k-1)*c2(l)
+ gradvalct2=gradvalct2+
+ & (l-1)*v1_kcc(l,k,j,itori1,itori)*c1(k)*c2(l-1)
+ enddo
+ enddo
+ gradvalct1=-gradvalct1*sinthet1
+ gradvalct2=-gradvalct2*sinthet2
+ sumvals=0.0d0
+ gradvalst1=0.0d0
+ gradvalst2=0.0d0
+ do k=1,nval
+ do l=1,nval
+ sumvals=sumvals+v2_kcc(l,k,j,itori1,itori)*c1(k)*c2(l)
+ gradvalst1=gradvalst1+
+ & (k-1)*v2_kcc(l,k,j,itori1,itori)*c1(k-1)*c2(l)
+ gradvalst2=gradvalst2+
+ & (l-1)*v2_kcc(l,k,j,itori1,itori)*c1(k)*c2(l-1)
+ enddo
+ enddo
+ gradvalst1=-gradvalst1*sinthet1
+ gradvalst2=-gradvalst2*sinthet2
+ if (lprn) write (iout,*)j,"sumvalc",sumvalc," sumvals",sumvals
+ etori=etori+sint1t2n*(sumvalc*cosphi+sumvals*sinphi)
+C glocig is the gradient local i site in gamma
+ glocig=glocig+j*sint1t2n*(sumvals*cosphi-sumvalc*sinphi)
+C now gradient over theta_1
+ glocit1=glocit1+sint1t2n*(gradvalct1*cosphi+gradvalst1*sinphi)
+ & +j*sint1t2n1*costhet1*sinthet2*(sumvalc*cosphi+sumvals*sinphi)
+ glocit2=glocit2+sint1t2n*(gradvalct2*cosphi+gradvalst2*sinphi)
+ & +j*sint1t2n1*sinthet1*costhet2*(sumvalc*cosphi+sumvals*sinphi)
+ enddo ! j
+ etors=etors+etori
+C derivative over gamma
+ gloc(i-3,icg)=gloc(i-3,icg)+wtor*glocig
+C derivative over theta1
+ gloc(nphi+i-3,icg)=gloc(nphi+i-3,icg)+wtor*glocit1
+C now derivative over theta2
+ gloc(nphi+i-2,icg)=gloc(nphi+i-2,icg)+wtor*glocit2
+ if (lprn) then
+ write (iout,*) i-2,i-1,itype(i-2),itype(i-1),itori,itori1,
+ & theta(i-1)*rad2deg,theta(i)*rad2deg,phii*rad2deg,etori
+ write (iout,*) "c1",(c1(k),k=0,nval),
+ & " c2",(c2(k),k=0,nval)
+ endif
+ enddo
+ return
+ end
+c---------------------------------------------------------------------------------------------
+ subroutine etor_constr(edihcnstr)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.VAR'
+ include 'COMMON.GEO'
+ include 'COMMON.LOCAL'
+ include 'COMMON.TORSION'
+ include 'COMMON.INTERACT'
+ include 'COMMON.DERIV'
+ include 'COMMON.CHAIN'
+ include 'COMMON.NAMES'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.FFIELD'
+ include 'COMMON.TORCNSTR'
+ include 'COMMON.BOUNDS'
+ include 'COMMON.CONTROL'
+! 6/20/98 - dihedral angle constraints
+ edihcnstr=0.0d0
+c do i=1,ndih_constr
+ if (raw_psipred) then
+ do i=idihconstr_start,idihconstr_end
+ itori=idih_constr(i)
+ phii=phi(itori)
+ gaudih_i=vpsipred(1,i)
+ gauder_i=0.0d0
+ do j=1,2
+ s = sdihed(j,i)
+ cos_i=(1.0d0-dcos(phii-phibound(j,i)))/s**2
+ dexpcos_i=dexp(-cos_i*cos_i)
+ gaudih_i=gaudih_i+vpsipred(j+1,i)*dexpcos_i
+ gauder_i=gauder_i-2*vpsipred(j+1,i)*dsin(phii-phibound(j,i))
+ & *cos_i*dexpcos_i/s**2
+ enddo
+ edihcnstr=edihcnstr-wdihc*dlog(gaudih_i)
+ gloc(itori-3,icg)=gloc(itori-3,icg)-wdihc*gauder_i/gaudih_i
+ if (energy_dec)
+ & write (iout,'(2i5,f8.3,f8.5,2(f8.5,2f8.3),f10.5)')
+ & i,itori,phii*rad2deg,vpsipred(1,i),vpsipred(2,i),
+ & phibound(1,i)*rad2deg,sdihed(1,i)*rad2deg,vpsipred(3,i),
+ & phibound(2,i)*rad2deg,sdihed(2,i)*rad2deg,
+ & -wdihc*dlog(gaudih_i)
+ enddo
+ else
+
+ do i=idihconstr_start,idihconstr_end
+ itori=idih_constr(i)
+ phii=phi(itori)
+ difi=pinorm(phii-phi0(i))
+ if (difi.gt.drange(i)) then
+ difi=difi-drange(i)
+ edihcnstr=edihcnstr+0.25d0*ftors(i)*difi**4
+ gloc(itori-3,icg)=gloc(itori-3,icg)+ftors(i)*difi**3
+ else if (difi.lt.-drange(i)) then
+ difi=difi+drange(i)
+ edihcnstr=edihcnstr+0.25d0*ftors(i)*difi**4
+ gloc(itori-3,icg)=gloc(itori-3,icg)+ftors(i)*difi**3
+ else
+ difi=0.0
+ endif
+ enddo
+
+ endif
+
+ return
+ end
+c----------------------------------------------------------------------------
+C The rigorous attempt to derive energy function
+ subroutine ebend_kcc(etheta)
+
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.VAR'
+ include 'COMMON.GEO'
+ include 'COMMON.LOCAL'
+ include 'COMMON.TORSION'
+ include 'COMMON.INTERACT'
+ include 'COMMON.DERIV'
+ include 'COMMON.CHAIN'
+ include 'COMMON.NAMES'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.FFIELD'
+ include 'COMMON.TORCNSTR'
+ include 'COMMON.CONTROL'
+ logical lprn
+ double precision thybt1(maxang_kcc)
+C Set lprn=.true. for debugging
+ lprn=energy_dec
+c lprn=.true.
+C print *,"wchodze kcc"
+ if (lprn) write (iout,*) "ebend_kcc tor_mode",tor_mode
+ etheta=0.0D0
+ do i=ithet_start,ithet_end
+c print *,i,itype(i-1),itype(i),itype(i-2)
+ if ((itype(i-1).eq.ntyp1).or.itype(i-2).eq.ntyp1
+ & .or.itype(i).eq.ntyp1) cycle
+ iti=iabs(itortyp(itype(i-1)))
+ sinthet=dsin(theta(i))
+ costhet=dcos(theta(i))
+ do j=1,nbend_kcc_Tb(iti)
+ thybt1(j)=v1bend_chyb(j,iti)
+ enddo
+ sumth1thyb=v1bend_chyb(0,iti)+
+ & tschebyshev(1,nbend_kcc_Tb(iti),thybt1(1),costhet)
+ if (lprn) write (iout,*) i-1,itype(i-1),iti,theta(i)*rad2deg,
+ & sumth1thyb
+ ihelp=nbend_kcc_Tb(iti)-1
+ gradthybt1=gradtschebyshev(0,ihelp,thybt1(1),costhet)
+ etheta=etheta+sumth1thyb
+C print *,sumth1thyb,gradthybt1,sinthet*(-0.5d0)
+ gloc(nphi+i-2,icg)=gloc(nphi+i-2,icg)-wang*gradthybt1*sinthet
+ enddo
+ return
+ end
+c-------------------------------------------------------------------------------------
+ subroutine etheta_constr(ethetacnstr)
+
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.VAR'
+ include 'COMMON.GEO'
+ include 'COMMON.LOCAL'
+ include 'COMMON.TORSION'
+ include 'COMMON.INTERACT'
+ include 'COMMON.DERIV'
+ include 'COMMON.CHAIN'
+ include 'COMMON.NAMES'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.FFIELD'
+ include 'COMMON.TORCNSTR'
+ include 'COMMON.CONTROL'
+ ethetacnstr=0.0d0
+C print *,ithetaconstr_start,ithetaconstr_end,"TU"
+ do i=ithetaconstr_start,ithetaconstr_end
+ itheta=itheta_constr(i)
+ thetiii=theta(itheta)
+ difi=pinorm(thetiii-theta_constr0(i))
+ if (difi.gt.theta_drange(i)) then
+ difi=difi-theta_drange(i)
+ ethetacnstr=ethetacnstr+0.25d0*for_thet_constr(i)*difi**4
+ gloc(itheta+nphi-2,icg)=gloc(itheta+nphi-2,icg)
+ & +for_thet_constr(i)*difi**3
+ else if (difi.lt.-drange(i)) then
+ difi=difi+drange(i)
+ ethetacnstr=ethetacnstr+0.25d0*for_thet_constr(i)*difi**4
+ gloc(itheta+nphi-2,icg)=gloc(itheta+nphi-2,icg)
+ & +for_thet_constr(i)*difi**3
+ else
+ difi=0.0
+ endif
+ if (energy_dec) then
+ write (iout,'(a6,2i5,4f8.3,2e14.5)') "ethetc",
+ & i,itheta,rad2deg*thetiii,
+ & rad2deg*theta_constr0(i), rad2deg*theta_drange(i),
+ & rad2deg*difi,0.25d0*for_thet_constr(i)*difi**4,
+ & gloc(itheta+nphi-2,icg)
+ endif
+ enddo
+ return
+ end
c------------------------------------------------------------------------------
subroutine eback_sc_corr(esccor)
c 7/21/2007 Correlations between the backbone-local and side-chain-local
C Set lprn=.true. for debugging
lprn=.false.
c lprn=.true.
-c write (iout,*) "EBACK_SC_COR",iphi_start,iphi_end,nterm_sccor
+c write (iout,*) "EBACK_SC_COR",itau_start,itau_end
esccor=0.0D0
- do i=iphi_start,iphi_end
- if (itype(i-2).eq.21 .or. itype(i-1).eq.21) cycle
+ do i=itau_start,itau_end
+ if ((itype(i-2).eq.ntyp1).or.(itype(i-1).eq.ntyp1)) cycle
esccor_ii=0.0D0
- itori=itype(i-2)
- itori1=itype(i-1)
+ isccori=isccortyp(itype(i-2))
+ isccori1=isccortyp(itype(i-1))
+c write (iout,*) "EBACK_SC_COR",i,nterm_sccor(isccori,isccori1)
phii=phi(i)
+ do intertyp=1,3 !intertyp
+cc Added 09 May 2012 (Adasko)
+cc Intertyp means interaction type of backbone mainchain correlation:
+c 1 = SC...Ca...Ca...Ca
+c 2 = Ca...Ca...Ca...SC
+c 3 = SC...Ca...Ca...SCi
gloci=0.0D0
- do j=1,nterm_sccor
- v1ij=v1sccor(j,itori,itori1)
- v2ij=v2sccor(j,itori,itori1)
- cosphi=dcos(j*phii)
- sinphi=dsin(j*phii)
+ if (((intertyp.eq.3).and.((itype(i-2).eq.10).or.
+ & (itype(i-1).eq.10).or.(itype(i-2).eq.ntyp1).or.
+ & (itype(i-1).eq.ntyp1)))
+ & .or. ((intertyp.eq.1).and.((itype(i-2).eq.10)
+ & .or.(itype(i-2).eq.ntyp1).or.(itype(i-1).eq.ntyp1)
+ & .or.(itype(i).eq.ntyp1)))
+ & .or.((intertyp.eq.2).and.((itype(i-1).eq.10).or.
+ & (itype(i-1).eq.ntyp1).or.(itype(i-2).eq.ntyp1).or.
+ & (itype(i-3).eq.ntyp1)))) cycle
+ if ((intertyp.eq.2).and.(i.eq.4).and.(itype(1).eq.ntyp1)) cycle
+ if ((intertyp.eq.1).and.(i.eq.nres).and.(itype(nres).eq.ntyp1))
+ & cycle
+ do j=1,nterm_sccor(isccori,isccori1)
+ v1ij=v1sccor(j,intertyp,isccori,isccori1)
+ v2ij=v2sccor(j,intertyp,isccori,isccori1)
+ cosphi=dcos(j*tauangle(intertyp,i))
+ sinphi=dsin(j*tauangle(intertyp,i))
esccor=esccor+v1ij*cosphi+v2ij*sinphi
gloci=gloci+j*(v2ij*cosphi-v1ij*sinphi)
enddo
+c write (iout,*) "EBACK_SC_COR",i,v1ij*cosphi+v2ij*sinphi,intertyp
+ gloc_sc(intertyp,i-3,icg)=gloc_sc(intertyp,i-3,icg)+wsccor*gloci
if (lprn)
& write (iout,'(2(a3,2x,i3,2x),2i3,6f8.3/26x,6f8.3/)')
- & restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,itori,itori1,
- & (v1sccor(j,itori,itori1),j=1,6),(v2sccor(j,itori,itori1),j=1,6)
+ & restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,isccori,isccori1,
+ & (v1sccor(j,intertyp,isccori,isccori1),j=1,6)
+ & ,(v2sccor(j,intertyp,isccori,isccori1),j=1,6)
gsccor_loc(i-3)=gsccor_loc(i-3)+gloci
+ enddo !intertyp
enddo
+
return
end
c----------------------------------------------------------------------------
include 'COMMON.DERIV'
include 'COMMON.INTERACT'
include 'COMMON.CONTACTS'
+ include 'COMMON.SHIELD'
double precision gx(3),gx1(3)
logical lprn
lprn=.false.
& i,num_cont_hb(i),(jcont_hb(j,i),facont_hb(j,i),
& j=1,num_cont_hb(i))
enddo
+ call flush(iout)
endif
- call flush(iout)
do i=1,ntask_cont_from
ncont_recv(i)=0
enddo
enddo
c write (iout,*) "ISEND ended"
c write (iout,*) "number of requests (nn)",ireq
- call flush(iout)
+c call flush(iout)
if (ireq.gt.0)
& call MPI_Waitall(ireq,req,status_array,ierr)
c write (iout,*)
nn=ncont_recv(ii)
c write (iout,*) "Receiving",nn," contacts from processor",iproc,
c & " of CONT_TO_COMM group"
- call flush(iout)
+c call flush(iout)
if (nn.gt.0) then
ireq=ireq+1
call MPI_Irecv(zapas_recv(1,1,ii),nn*max_dim,
gacontp_hb3(3,nnn,ii)=zapas_recv(26,i,iii)
enddo
enddo
- call flush(iout)
if (lprn) then
write (iout,'(a)') 'Contact function values after receive:'
do i=nnt,nct-2
& i,num_cont_hb(i),(jcont_hb(j,i),facont_hb(j,i),
& j=1,num_cont_hb(i))
enddo
+ call flush(iout)
endif
ecorr=0.0D0
C Remove the loop below after debugging !!!
jp1=iabs(j1)
c write (iout,*) 'i=',i,' j=',j,' i1=',i1,' j1=',j1,
c & ' jj=',jj,' kk=',kk
+c call flush(iout)
if ((j.gt.0 .and. j1.gt.0 .or. j.gt.0 .and. j1.lt.0
& .or. j.lt.0 .and. j1.gt.0) .and.
& (jp1.eq.jp+1 .or. jp1.eq.jp-1)) then
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
& j=1,num_cont_hb(i))
enddo
endif
- call flush(iout)
do i=1,ntask_cont_from
ncont_recv(i)=0
enddo
enddo
c write (iout,*) "ISEND ended"
c write (iout,*) "number of requests (nn)",ireq
- call flush(iout)
+c call flush(iout)
if (ireq.gt.0)
& call MPI_Waitall(ireq,req,status_array,ierr)
c write (iout,*)
nn=ncont_recv(ii)
c write (iout,*) "Receiving",nn," contacts from processor",iproc,
c & " of CONT_TO_COMM group"
- call flush(iout)
+c call flush(iout)
if (nn.gt.0) then
ireq=ireq+1
call MPI_Irecv(zapas_recv(1,1,ii),nn*max_dim,
enddo
enddo
enddo
- call flush(iout)
if (lprn) then
write (iout,'(a)') 'Contact function values after receive:'
do i=nnt,nct-2
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)
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)
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
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
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
& auxmat(2,2)
iti1 = itortyp(itype(i+1))
if (j.lt.nres-1) then
- itj1 = itortyp(itype(j+1))
+ itj1 = itype2loc(itype(j+1))
else
- itj1=ntortyp+1
+ itj1=nloctyp
endif
do iii=1,2
dipi(iii,1)=Ub2(iii,i)
dipderi(iii)=Ub2der(iii,i)
- dipi(iii,2)=b1(iii,iti1)
+ dipi(iii,2)=b1(iii,i+1)
dipj(iii,1)=Ub2(iii,j)
dipderj(iii)=Ub2der(iii,j)
- dipj(iii,2)=b1(iii,itj1)
+ dipj(iii,2)=b1(iii,j+1)
enddo
kkk=0
do iii=1,2
if (l.eq.j+1) then
C parallel orientation of the two CA-CA-CA frames.
if (i.gt.1) then
- iti=itortyp(itype(i))
+ iti=itype2loc(itype(i))
else
- iti=ntortyp+1
+ iti=nloctyp
endif
- itk1=itortyp(itype(k+1))
- itj=itortyp(itype(j))
+ itk1=itype2loc(itype(k+1))
+ itj=itype2loc(itype(j))
if (l.lt.nres-1) then
- itl1=itortyp(itype(l+1))
+ itl1=itype2loc(itype(l+1))
else
- itl1=ntortyp+1
+ itl1=nloctyp
endif
C A1 kernel(j+1) A2T
cd do iii=1,2
call transpose2(EUg(1,1,k),auxmat(1,1))
call matmat2(auxmat(1,1),AEA(1,1,1),EAEA(1,1,1))
call matmat2(auxmat(1,1),AEAderg(1,1,1),EAEAderg(1,1,2,1))
+C AL 4/16/16: Derivatives of the quantitied related to matrices C, D, and E
+c in theta; to be sriten later.
+c#ifdef NEWCORR
+c call transpose2(gtEE(1,1,k),auxmat(1,1))
+c call matmat2(auxmat(1,1),AEA(1,1,1),EAEAdert(1,1,1,1))
+c call transpose2(EUg(1,1,k),auxmat(1,1))
+c call matmat2(auxmat(1,1),AEAdert(1,1,1),EAEAdert(1,1,2,1))
+c#endif
do iii=1,2
do kkk=1,5
do lll=1,3
C indluded.
IF (wcorr5.gt.0.0d0 .or. wcorr6.gt.0.0d0) THEN
call transpose2(AEA(1,1,1),auxmat(1,1))
- call matvec2(auxmat(1,1),b1(1,iti),AEAb1(1,1,1))
+ call matvec2(auxmat(1,1),b1(1,i),AEAb1(1,1,1))
call matvec2(auxmat(1,1),Ub2(1,i),AEAb2(1,1,1))
call matvec2(auxmat(1,1),Ub2der(1,i),AEAb2derg(1,2,1,1))
call transpose2(AEAderg(1,1,1),auxmat(1,1))
- call matvec2(auxmat(1,1),b1(1,iti),AEAb1derg(1,1,1))
+ call matvec2(auxmat(1,1),b1(1,i),AEAb1derg(1,1,1))
call matvec2(auxmat(1,1),Ub2(1,i),AEAb2derg(1,1,1,1))
- call matvec2(AEA(1,1,1),b1(1,itk1),AEAb1(1,2,1))
- call matvec2(AEAderg(1,1,1),b1(1,itk1),AEAb1derg(1,2,1))
+ call matvec2(AEA(1,1,1),b1(1,k+1),AEAb1(1,2,1))
+ call matvec2(AEAderg(1,1,1),b1(1,k+1),AEAb1derg(1,2,1))
call matvec2(AEA(1,1,1),Ub2(1,k+1),AEAb2(1,2,1))
call matvec2(AEAderg(1,1,1),Ub2(1,k+1),AEAb2derg(1,1,2,1))
call matvec2(AEA(1,1,1),Ub2der(1,k+1),AEAb2derg(1,2,2,1))
call transpose2(AEA(1,1,2),auxmat(1,1))
- call matvec2(auxmat(1,1),b1(1,itj),AEAb1(1,1,2))
+ call matvec2(auxmat(1,1),b1(1,j),AEAb1(1,1,2))
call matvec2(auxmat(1,1),Ub2(1,j),AEAb2(1,1,2))
call matvec2(auxmat(1,1),Ub2der(1,j),AEAb2derg(1,2,1,2))
call transpose2(AEAderg(1,1,2),auxmat(1,1))
- call matvec2(auxmat(1,1),b1(1,itj),AEAb1derg(1,1,2))
+ call matvec2(auxmat(1,1),b1(1,j),AEAb1derg(1,1,2))
call matvec2(auxmat(1,1),Ub2(1,j),AEAb2derg(1,1,1,2))
- call matvec2(AEA(1,1,2),b1(1,itl1),AEAb1(1,2,2))
- call matvec2(AEAderg(1,1,2),b1(1,itl1),AEAb1derg(1,2,2))
+ call matvec2(AEA(1,1,2),b1(1,l+1),AEAb1(1,2,2))
+ call matvec2(AEAderg(1,1,2),b1(1,l+1),AEAb1derg(1,2,2))
call matvec2(AEA(1,1,2),Ub2(1,l+1),AEAb2(1,2,2))
call matvec2(AEAderg(1,1,2),Ub2(1,l+1),AEAb2derg(1,1,2,2))
call matvec2(AEA(1,1,2),Ub2der(1,l+1),AEAb2derg(1,2,2,2))
do kkk=1,5
do lll=1,3
call transpose2(AEAderx(1,1,lll,kkk,iii,1),auxmat(1,1))
- call matvec2(auxmat(1,1),b1(1,iti),
+ call matvec2(auxmat(1,1),b1(1,i),
& AEAb1derx(1,lll,kkk,iii,1,1))
call matvec2(auxmat(1,1),Ub2(1,i),
& AEAb2derx(1,lll,kkk,iii,1,1))
- call matvec2(AEAderx(1,1,lll,kkk,iii,1),b1(1,itk1),
+ call matvec2(AEAderx(1,1,lll,kkk,iii,1),b1(1,k+1),
& AEAb1derx(1,lll,kkk,iii,2,1))
call matvec2(AEAderx(1,1,lll,kkk,iii,1),Ub2(1,k+1),
& AEAb2derx(1,lll,kkk,iii,2,1))
call transpose2(AEAderx(1,1,lll,kkk,iii,2),auxmat(1,1))
- call matvec2(auxmat(1,1),b1(1,itj),
+ call matvec2(auxmat(1,1),b1(1,j),
& AEAb1derx(1,lll,kkk,iii,1,2))
call matvec2(auxmat(1,1),Ub2(1,j),
& AEAb2derx(1,lll,kkk,iii,1,2))
- call matvec2(AEAderx(1,1,lll,kkk,iii,2),b1(1,itl1),
+ call matvec2(AEAderx(1,1,lll,kkk,iii,2),b1(1,l+1),
& AEAb1derx(1,lll,kkk,iii,2,2))
call matvec2(AEAderx(1,1,lll,kkk,iii,2),Ub2(1,l+1),
& AEAb2derx(1,lll,kkk,iii,2,2))
else
C Antiparallel orientation of the two CA-CA-CA frames.
if (i.gt.1) then
- iti=itortyp(itype(i))
+ iti=itype2loc(itype(i))
else
- iti=ntortyp+1
+ iti=nloctyp
endif
- itk1=itortyp(itype(k+1))
- itl=itortyp(itype(l))
- itj=itortyp(itype(j))
+ itk1=itype2loc(itype(k+1))
+ itl=itype2loc(itype(l))
+ itj=itype2loc(itype(j))
if (j.lt.nres-1) then
- itj1=itortyp(itype(j+1))
+ itj1=itype2loc(itype(j+1))
else
- itj1=ntortyp+1
+ itj1=nloctyp
endif
C A2 kernel(j-1)T A1T
call kernel(aa1(1,1),aa2t(1,1),a_chuj_der(1,1,1,1,jj,i),
IF (wcorr5.gt.0.0d0 .or. wcorr6.gt.0.0d0 .or.
& (wturn6.gt.0.0d0 .and. j.eq.i+4 .and. l.eq.i+3)) THEN
call transpose2(AEA(1,1,1),auxmat(1,1))
- call matvec2(auxmat(1,1),b1(1,iti),AEAb1(1,1,1))
+ call matvec2(auxmat(1,1),b1(1,i),AEAb1(1,1,1))
call matvec2(auxmat(1,1),Ub2(1,i),AEAb2(1,1,1))
call matvec2(auxmat(1,1),Ub2der(1,i),AEAb2derg(1,2,1,1))
call transpose2(AEAderg(1,1,1),auxmat(1,1))
- call matvec2(auxmat(1,1),b1(1,iti),AEAb1derg(1,1,1))
+ call matvec2(auxmat(1,1),b1(1,i),AEAb1derg(1,1,1))
call matvec2(auxmat(1,1),Ub2(1,i),AEAb2derg(1,1,1,1))
- call matvec2(AEA(1,1,1),b1(1,itk1),AEAb1(1,2,1))
- call matvec2(AEAderg(1,1,1),b1(1,itk1),AEAb1derg(1,2,1))
+ call matvec2(AEA(1,1,1),b1(1,k+1),AEAb1(1,2,1))
+ call matvec2(AEAderg(1,1,1),b1(1,k+1),AEAb1derg(1,2,1))
call matvec2(AEA(1,1,1),Ub2(1,k+1),AEAb2(1,2,1))
call matvec2(AEAderg(1,1,1),Ub2(1,k+1),AEAb2derg(1,1,2,1))
call matvec2(AEA(1,1,1),Ub2der(1,k+1),AEAb2derg(1,2,2,1))
call transpose2(AEA(1,1,2),auxmat(1,1))
- call matvec2(auxmat(1,1),b1(1,itj1),AEAb1(1,1,2))
+ call matvec2(auxmat(1,1),b1(1,j+1),AEAb1(1,1,2))
call matvec2(auxmat(1,1),Ub2(1,l),AEAb2(1,1,2))
call matvec2(auxmat(1,1),Ub2der(1,l),AEAb2derg(1,2,1,2))
call transpose2(AEAderg(1,1,2),auxmat(1,1))
- call matvec2(auxmat(1,1),b1(1,itl),AEAb1(1,1,2))
+ call matvec2(auxmat(1,1),b1(1,l),AEAb1(1,1,2))
call matvec2(auxmat(1,1),Ub2(1,l),AEAb2derg(1,1,1,2))
- call matvec2(AEA(1,1,2),b1(1,itj1),AEAb1(1,2,2))
- call matvec2(AEAderg(1,1,2),b1(1,itj1),AEAb1derg(1,2,2))
+ call matvec2(AEA(1,1,2),b1(1,j+1),AEAb1(1,2,2))
+ call matvec2(AEAderg(1,1,2),b1(1,j+1),AEAb1derg(1,2,2))
call matvec2(AEA(1,1,2),Ub2(1,j),AEAb2(1,2,2))
call matvec2(AEAderg(1,1,2),Ub2(1,j),AEAb2derg(1,1,2,2))
call matvec2(AEA(1,1,2),Ub2der(1,j),AEAb2derg(1,2,2,2))
do kkk=1,5
do lll=1,3
call transpose2(AEAderx(1,1,lll,kkk,iii,1),auxmat(1,1))
- call matvec2(auxmat(1,1),b1(1,iti),
+ call matvec2(auxmat(1,1),b1(1,i),
& AEAb1derx(1,lll,kkk,iii,1,1))
call matvec2(auxmat(1,1),Ub2(1,i),
& AEAb2derx(1,lll,kkk,iii,1,1))
- call matvec2(AEAderx(1,1,lll,kkk,iii,1),b1(1,itk1),
+ call matvec2(AEAderx(1,1,lll,kkk,iii,1),b1(1,k+1),
& AEAb1derx(1,lll,kkk,iii,2,1))
call matvec2(AEAderx(1,1,lll,kkk,iii,1),Ub2(1,k+1),
& AEAb2derx(1,lll,kkk,iii,2,1))
call transpose2(AEAderx(1,1,lll,kkk,iii,2),auxmat(1,1))
- call matvec2(auxmat(1,1),b1(1,itl),
+ call matvec2(auxmat(1,1),b1(1,l),
& AEAb1derx(1,lll,kkk,iii,1,2))
call matvec2(auxmat(1,1),Ub2(1,l),
& AEAb2derx(1,lll,kkk,iii,1,2))
- call matvec2(AEAderx(1,1,lll,kkk,iii,2),b1(1,itj1),
+ call matvec2(AEAderx(1,1,lll,kkk,iii,2),b1(1,j+1),
& AEAb1derx(1,lll,kkk,iii,2,2))
call matvec2(AEAderx(1,1,lll,kkk,iii,2),Ub2(1,j),
& AEAb2derx(1,lll,kkk,iii,2,2))
if (l.eq.j+1) then
gcorr_loc(l-1)=gcorr_loc(l-1)
& -ekont*(EAEAderg(1,1,2,1)+EAEAderg(2,2,2,1))
+C Al 4/16/16: Derivatives in theta, to be added later.
+c#ifdef NEWCORR
+c gcorr_loc(nphi+l-1)=gcorr_loc(nphi+l-1)
+c & -ekont*(EAEAdert(1,1,2,1)+EAEAdert(2,2,2,1))
+c#endif
else
gcorr_loc(j-1)=gcorr_loc(j-1)
& -ekont*(EAEAderg(1,1,2,1)+EAEAderg(2,2,2,1))
+c#ifdef NEWCORR
+c gcorr_loc(nphi+j-1)=gcorr_loc(nphi+j-1)
+c & -ekont*(EAEAdert(1,1,2,1)+EAEAdert(2,2,2,1))
+c#endif
endif
do iii=1,2
do kkk=1,5
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
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)
- eello5_2=scalar2(AEAb1(1,2,1),b1(1,itk))
+ eello5_2=scalar2(AEAb1(1,2,1),b1(1,k))
& -0.5d0*scalar2(vv(1),Ctobr(1,k))
C Explicit gradient in virtual-dihedral angles.
g_corr5_loc(k-1)=g_corr5_loc(k-1)
vv(2)=pizda(2,1)-pizda(1,2)
if (l.eq.j+1) then
g_corr5_loc(l-1)=g_corr5_loc(l-1)
- & +ekont*(scalar2(AEAb1derg(1,2,1),b1(1,itk))
+ & +ekont*(scalar2(AEAb1derg(1,2,1),b1(1,k))
& -0.5d0*scalar2(vv(1),Ctobr(1,k)))
else
g_corr5_loc(j-1)=g_corr5_loc(j-1)
- & +ekont*(scalar2(AEAb1derg(1,2,1),b1(1,itk))
+ & +ekont*(scalar2(AEAb1derg(1,2,1),b1(1,k))
& -0.5d0*scalar2(vv(1),Ctobr(1,k)))
endif
C Cartesian gradient
vv(1)=pizda(1,1)+pizda(2,2)
vv(2)=pizda(2,1)-pizda(1,2)
derx(lll,kkk,iii)=derx(lll,kkk,iii)
- & +scalar2(AEAb1derx(1,lll,kkk,iii,2,1),b1(1,itk))
+ & +scalar2(AEAb1derx(1,lll,kkk,iii,2,1),b1(1,k))
& -0.5d0*scalar2(vv(1),Ctobr(1,k))
enddo
enddo
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)
- eello5_4=scalar2(AEAb1(1,2,2),b1(1,itl))
+ eello5_4=scalar2(AEAb1(1,2,2),b1(1,l))
& -0.5d0*scalar2(vv(1),Ctobr(1,l))
C Explicit gradient in virtual-dihedral angles.
g_corr5_loc(l-1)=g_corr5_loc(l-1)
vv(1)=pizda(1,1)+pizda(2,2)
vv(2)=pizda(2,1)-pizda(1,2)
g_corr5_loc(k-1)=g_corr5_loc(k-1)
- & +ekont*(scalar2(AEAb1derg(1,2,2),b1(1,itl))
+ & +ekont*(scalar2(AEAb1derg(1,2,2),b1(1,l))
& -0.5d0*scalar2(vv(1),Ctobr(1,l)))
C Cartesian gradient
do iii=1,2
vv(1)=pizda(1,1)+pizda(2,2)
vv(2)=pizda(2,1)-pizda(1,2)
derx(lll,kkk,iii)=derx(lll,kkk,iii)
- & +scalar2(AEAb1derx(1,lll,kkk,iii,2,2),b1(1,itl))
+ & +scalar2(AEAb1derx(1,lll,kkk,iii,2,2),b1(1,l))
& -0.5d0*scalar2(vv(1),Ctobr(1,l))
enddo
enddo
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)
- eello5_4=scalar2(AEAb1(1,2,2),b1(1,itj))
+ eello5_4=scalar2(AEAb1(1,2,2),b1(1,j))
& -0.5d0*scalar2(vv(1),Ctobr(1,j))
C Explicit gradient in virtual-dihedral angles.
g_corr5_loc(j-1)=g_corr5_loc(j-1)
vv(1)=pizda(1,1)+pizda(2,2)
vv(2)=pizda(2,1)-pizda(1,2)
g_corr5_loc(k-1)=g_corr5_loc(k-1)
- & +ekont*(scalar2(AEAb1derg(1,2,2),b1(1,itj))
+ & +ekont*(scalar2(AEAb1derg(1,2,2),b1(1,j))
& -0.5d0*scalar2(vv(1),Ctobr(1,j)))
C Cartesian gradient
do iii=1,2
vv(1)=pizda(1,1)+pizda(2,2)
vv(2)=pizda(2,1)-pizda(1,2)
derx(lll,kkk,3-iii)=derx(lll,kkk,3-iii)
- & +scalar2(AEAb1derx(1,lll,kkk,iii,2,2),b1(1,itj))
+ & +scalar2(AEAb1derx(1,lll,kkk,iii,2,2),b1(1,j))
& -0.5d0*scalar2(vv(1),Ctobr(1,j))
enddo
enddo
cold ghalf=0.5d0*eel5*eij*gacont_hbr(ll,kk,k)
cgrad ghalf=0.5d0*ggg2(ll)
cd ghalf=0.0d0
- gradcorr5(ll,k)=gradcorr5(ll,k)+ghalf+ekont*derx(ll,2,2)
+ gradcorr5(ll,k)=gradcorr5(ll,k)+ekont*derx(ll,2,2)
gradcorr5(ll,k+1)=gradcorr5(ll,k+1)+ekont*derx(ll,3,2)
- gradcorr5(ll,l)=gradcorr5(ll,l)+ghalf+ekont*derx(ll,4,2)
+ gradcorr5(ll,l)=gradcorr5(ll,l)+ekont*derx(ll,4,2)
gradcorr5(ll,l1)=gradcorr5(ll,l1)+ekont*derx(ll,5,2)
gradcorr5_long(ll,l)=gradcorr5_long(ll,l)+gradcorr5kl
gradcorr5_long(ll,k)=gradcorr5_long(ll,k)-gradcorr5kl
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))
vv1(1)=pizda1(1,1)-pizda1(2,2)
vv1(2)=pizda1(1,2)+pizda1(2,1)
s4=0.5d0*scalar2(vv1(1),Dtobr2(1,i))
- vv(1)=AEAb1(1,2,imat)*b1(1,itk)-AEAb1(2,2,imat)*b1(2,itk)
- vv(2)=AEAb1(1,2,imat)*b1(2,itk)+AEAb1(2,2,imat)*b1(1,itk)
+ vv(1)=AEAb1(1,2,imat)*b1(1,k)-AEAb1(2,2,imat)*b1(2,k)
+ vv(2)=AEAb1(1,2,imat)*b1(2,k)+AEAb1(2,2,imat)*b1(1,k)
s5=scalar2(vv(1),Dtobr2(1,i))
cd write (2,*) 's1',s1,' s2',s2,' s3',s3,' s4', s4,' s5',s5
eello6_graph1=-0.5d0*(s1+s2+s3+s4+s5)
call matmat2(AEAderg(1,1,imat),auxmat(1,1),pizda1(1,1))
vv1(1)=pizda1(1,1)-pizda1(2,2)
vv1(2)=pizda1(1,2)+pizda1(2,1)
- vv(1)=AEAb1derg(1,2,imat)*b1(1,itk)-AEAb1derg(2,2,imat)*b1(2,itk)
- vv(2)=AEAb1derg(1,2,imat)*b1(2,itk)+AEAb1derg(2,2,imat)*b1(1,itk)
+ vv(1)=AEAb1derg(1,2,imat)*b1(1,k)-AEAb1derg(2,2,imat)*b1(2,k)
+ vv(2)=AEAb1derg(1,2,imat)*b1(2,k)+AEAb1derg(2,2,imat)*b1(1,k)
if (l.eq.j+1) then
g_corr6_loc(l-1)=g_corr6_loc(l-1)
& +ekont*(-0.5d0*(scalar2(AEAb1derg(1,2,imat),CUgb2(1,i))
vv1(1)=pizda1(1,1)-pizda1(2,2)
vv1(2)=pizda1(1,2)+pizda1(2,1)
s4=0.5d0*scalar2(vv1(1),Dtobr2(1,i))
- vv(1)=AEAb1derx(1,lll,kkk,iii,2,imat)*b1(1,itk)
- & -AEAb1derx(2,lll,kkk,iii,2,imat)*b1(2,itk)
- vv(2)=AEAb1derx(1,lll,kkk,iii,2,imat)*b1(2,itk)
- & +AEAb1derx(2,lll,kkk,iii,2,imat)*b1(1,itk)
+ vv(1)=AEAb1derx(1,lll,kkk,iii,2,imat)*b1(1,k)
+ & -AEAb1derx(2,lll,kkk,iii,2,imat)*b1(2,k)
+ vv(2)=AEAb1derx(1,lll,kkk,iii,2,imat)*b1(2,k)
+ & +AEAb1derx(2,lll,kkk,iii,2,imat)*b1(1,k)
s5=scalar2(vv(1),Dtobr2(1,i))
derx(lll,kkk,ind)=derx(lll,kkk,ind)-0.5d0*(s1+s2+s3+s4+s5)
enddo
include 'COMMON.GEO'
logical swap
double precision vv(2),pizda(2,2),auxmat(2,2),auxvec(2),
- & auxvec1(2),auxvec2(1),auxmat1(2,2)
+ & auxvec1(2),auxvec2(2),auxmat1(2,2)
logical lprn
common /kutas/ lprn
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
C o o C
C \ /l\ /j\ / C
C \ / \ / \ / C
-C o| o | | o |o C
+C o| o | | o |o C
C \ j|/k\| \ |/k\|l C
C \ / \ \ / \ C
C o o C
-C i i C
-C C
+C i i C
+C C
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
cd write (2,*) 'eello6_graph2: i,',i,' j',j,' k',k,' l',l
C AL 7/4/01 s1 would occur in the sixth-order moment,
double precision vv(2),pizda(2,2),auxmat(2,2),auxvec(2)
logical swap
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
-C C
+C C
C Parallel Antiparallel C
C C
-C o o C
+C o o C
C /l\ / \ /j\ C
C / \ / \ / \ C
C /| o |o o| o |\ C
C energy moment and not to the cluster cumulant.
iti=itortyp(itype(i))
if (j.lt.nres-1) then
- itj1=itortyp(itype(j+1))
+ itj1=itype2loc(itype(j+1))
else
- itj1=ntortyp+1
+ itj1=nloctyp
endif
- itk=itortyp(itype(k))
- itk1=itortyp(itype(k+1))
+ itk=itype2loc(itype(k))
+ itk1=itype2loc(itype(k+1))
if (l.lt.nres-1) then
- itl1=itortyp(itype(l+1))
+ itl1=itype2loc(itype(l+1))
else
- itl1=ntortyp+1
+ itl1=nloctyp
endif
#ifdef MOMENT
s1=dip(4,jj,i)*dip(4,kk,k)
#endif
- call matvec2(AECA(1,1,1),b1(1,itk1),auxvec(1))
- s2=0.5d0*scalar2(b1(1,itk),auxvec(1))
- call matvec2(AECA(1,1,2),b1(1,itl1),auxvec(1))
- s3=0.5d0*scalar2(b1(1,itj1),auxvec(1))
- call transpose2(EE(1,1,itk),auxmat(1,1))
+ call matvec2(AECA(1,1,1),b1(1,k+1),auxvec(1))
+ s2=0.5d0*scalar2(b1(1,k),auxvec(1))
+ call matvec2(AECA(1,1,2),b1(1,l+1),auxvec(1))
+ s3=0.5d0*scalar2(b1(1,j+1),auxvec(1))
+ call transpose2(EE(1,1,k),auxmat(1,1))
call matmat2(auxmat(1,1),AECA(1,1,1),pizda(1,1))
vv(1)=pizda(1,1)+pizda(2,2)
vv(2)=pizda(2,1)-pizda(1,2)
#endif
c eello6_graph3=-s4
C Derivatives in gamma(k-1)
- call matvec2(AECAderg(1,1,2),b1(1,itl1),auxvec(1))
- s3=0.5d0*scalar2(b1(1,itj1),auxvec(1))
+ call matvec2(AECAderg(1,1,2),b1(1,l+1),auxvec(1))
+ s3=0.5d0*scalar2(b1(1,j+1),auxvec(1))
s4=-0.25d0*scalar2(vv(1),Ctobrder(1,k))
g_corr6_loc(k-1)=g_corr6_loc(k-1)-ekont*(s3+s4)
C Derivatives in gamma(l-1)
- call matvec2(AECAderg(1,1,1),b1(1,itk1),auxvec(1))
- s2=0.5d0*scalar2(b1(1,itk),auxvec(1))
+ call matvec2(AECAderg(1,1,1),b1(1,k+1),auxvec(1))
+ s2=0.5d0*scalar2(b1(1,k),auxvec(1))
call matmat2(auxmat(1,1),AECAderg(1,1,1),pizda(1,1))
vv(1)=pizda(1,1)+pizda(2,2)
vv(2)=pizda(2,1)-pizda(1,2)
s1=dip(4,jj,i)*dipderx(lll,kkk,4,kk,k)
endif
#endif
- call matvec2(AECAderx(1,1,lll,kkk,iii,1),b1(1,itk1),
+ call matvec2(AECAderx(1,1,lll,kkk,iii,1),b1(1,k+1),
& auxvec(1))
- s2=0.5d0*scalar2(b1(1,itk),auxvec(1))
- call matvec2(AECAderx(1,1,lll,kkk,iii,2),b1(1,itl1),
+ s2=0.5d0*scalar2(b1(1,k),auxvec(1))
+ call matvec2(AECAderx(1,1,lll,kkk,iii,2),b1(1,l+1),
& auxvec(1))
- s3=0.5d0*scalar2(b1(1,itj1),auxvec(1))
+ s3=0.5d0*scalar2(b1(1,j+1),auxvec(1))
call matmat2(auxmat(1,1),AECAderx(1,1,lll,kkk,iii,1),
& pizda(1,1))
vv(1)=pizda(1,1)+pizda(2,2)
& auxvec1(2),auxmat1(2,2)
logical swap
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
-C C
+C C
C Parallel Antiparallel C
C C
C o o C
C / \ / \ / \ C
C /| o |o o| o |\ C
C \ j|/k\| \ |/k\|l C
-C \ / \ \ / \ C
+C \ / \ \ / \ C
C o \ o \ C
C i i C
-C C
+C C
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
C
C 4/7/01 AL Component s1 was removed, because it pertains to the respective
C energy moment and not to the cluster cumulant.
cd write (2,*) 'eello_graph4: wturn6',wturn6
- iti=itortyp(itype(i))
- itj=itortyp(itype(j))
+ iti=itype2loc(itype(i))
+ itj=itype2loc(itype(j))
if (j.lt.nres-1) then
- itj1=itortyp(itype(j+1))
+ itj1=itype2loc(itype(j+1))
else
- itj1=ntortyp+1
+ itj1=nloctyp
endif
- itk=itortyp(itype(k))
+ itk=itype2loc(itype(k))
if (k.lt.nres-1) then
- itk1=itortyp(itype(k+1))
+ itk1=itype2loc(itype(k+1))
else
- itk1=ntortyp+1
+ itk1=nloctyp
endif
- itl=itortyp(itype(l))
+ itl=itype2loc(itype(l))
if (l.lt.nres-1) then
- itl1=itortyp(itype(l+1))
+ itl1=itype2loc(itype(l+1))
else
- itl1=ntortyp+1
+ itl1=nloctyp
endif
cd write (2,*) 'eello6_graph4:','i',i,' j',j,' k',k,' l',l
cd write (2,*) 'iti',iti,' itj',itj,' itj1',itj1,' itk',itk,
call matvec2(AECA(1,1,imat),Ub2(1,k),auxvec(1))
s2=0.5d0*scalar2(Ub2(1,i),auxvec(1))
if (j.eq.l+1) then
- call matvec2(ADtEA1(1,1,3-imat),b1(1,itj1),auxvec1(1))
- s3=-0.5d0*scalar2(b1(1,itj),auxvec1(1))
+ call matvec2(ADtEA1(1,1,3-imat),b1(1,j+1),auxvec1(1))
+ s3=-0.5d0*scalar2(b1(1,j),auxvec1(1))
else
- call matvec2(ADtEA1(1,1,3-imat),b1(1,itl1),auxvec1(1))
- s3=-0.5d0*scalar2(b1(1,itl),auxvec1(1))
+ call matvec2(ADtEA1(1,1,3-imat),b1(1,l+1),auxvec1(1))
+ s3=-0.5d0*scalar2(b1(1,l),auxvec1(1))
endif
call transpose2(EUg(1,1,k),auxmat(1,1))
call matmat2(AECA(1,1,imat),auxmat(1,1),pizda(1,1))
#endif
s2=0.5d0*scalar2(Ub2der(1,i),auxvec(1))
if (j.eq.l+1) then
- call matvec2(ADtEA1derg(1,1,1,3-imat),b1(1,itj1),auxvec1(1))
- s3=-0.5d0*scalar2(b1(1,itj),auxvec1(1))
+ call matvec2(ADtEA1derg(1,1,1,3-imat),b1(1,j+1),auxvec1(1))
+ s3=-0.5d0*scalar2(b1(1,j),auxvec1(1))
else
- call matvec2(ADtEA1derg(1,1,1,3-imat),b1(1,itl1),auxvec1(1))
- s3=-0.5d0*scalar2(b1(1,itl),auxvec1(1))
+ call matvec2(ADtEA1derg(1,1,1,3-imat),b1(1,l+1),auxvec1(1))
+ s3=-0.5d0*scalar2(b1(1,l),auxvec1(1))
endif
s4=0.25d0*scalar2(vv(1),Dtobr2der(1,i))
if (wturn6.gt.0.0d0 .and. k.eq.l+4 .and. i.eq.j+2) then
call matvec2(AECA(1,1,imat),Ub2der(1,k),auxvec1(1))
s2=0.5d0*scalar2(Ub2(1,i),auxvec1(1))
if (j.eq.l+1) then
- call matvec2(ADtEA1derg(1,1,2,3-imat),b1(1,itj1),auxvec1(1))
- s3=-0.5d0*scalar2(b1(1,itj),auxvec1(1))
+ call matvec2(ADtEA1derg(1,1,2,3-imat),b1(1,j+1),auxvec1(1))
+ s3=-0.5d0*scalar2(b1(1,j),auxvec1(1))
else
- call matvec2(ADtEA1derg(1,1,2,3-imat),b1(1,itl1),auxvec1(1))
- s3=-0.5d0*scalar2(b1(1,itl),auxvec1(1))
+ call matvec2(ADtEA1derg(1,1,2,3-imat),b1(1,l+1),auxvec1(1))
+ s3=-0.5d0*scalar2(b1(1,l),auxvec1(1))
endif
call transpose2(EUgder(1,1,k),auxmat1(1,1))
call matmat2(AECA(1,1,imat),auxmat1(1,1),pizda(1,1))
s2=0.5d0*scalar2(Ub2(1,i),auxvec(1))
if (j.eq.l+1) then
call matvec2(ADtEA1derx(1,1,lll,kkk,iii,3-imat),
- & b1(1,itj1),auxvec(1))
- s3=-0.5d0*scalar2(b1(1,itj),auxvec(1))
+ & b1(1,j+1),auxvec(1))
+ s3=-0.5d0*scalar2(b1(1,j),auxvec(1))
else
call matvec2(ADtEA1derx(1,1,lll,kkk,iii,3-imat),
- & b1(1,itl1),auxvec(1))
- s3=-0.5d0*scalar2(b1(1,itl),auxvec(1))
+ & b1(1,l+1),auxvec(1))
+ s3=-0.5d0*scalar2(b1(1,l),auxvec(1))
endif
call matmat2(AECAderx(1,1,lll,kkk,iii,imat),auxmat(1,1),
& pizda(1,1))
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
#ifdef MOMENT
call transpose2(AEA(1,1,1),auxmat(1,1))
call matmat2(EUg(1,1,i+1),auxmat(1,1),auxmat(1,1))
- ss1=scalar2(Ub2(1,i+2),b1(1,itl))
+ ss1=scalar2(Ub2(1,i+2),b1(1,l))
s1 = (auxmat(1,1)+auxmat(2,2))*ss1
#endif
- call matvec2(EUg(1,1,i+2),b1(1,itl),vtemp1(1))
+ call matvec2(EUg(1,1,i+2),b1(1,l),vtemp1(1))
call matvec2(AEA(1,1,1),vtemp1(1),vtemp1(1))
- s2 = scalar2(b1(1,itk),vtemp1(1))
+ s2 = scalar2(b1(1,k),vtemp1(1))
#ifdef MOMENT
call transpose2(AEA(1,1,2),atemp(1,1))
call matmat2(atemp(1,1),EUg(1,1,i+4),atemp(1,1))
- call matvec2(Ug2(1,1,i+2),dd(1,1,itk1),vtemp2(1))
- s8 = -(atemp(1,1)+atemp(2,2))*scalar2(cc(1,1,itl),vtemp2(1))
+ call matvec2(Ug2(1,1,i+2),dd(1,1,k+1),vtemp2(1))
+ s8 = -(atemp(1,1)+atemp(2,2))*scalar2(cc(1,1,l),vtemp2(1))
#endif
call matmat2(EUg(1,1,i+3),AEA(1,1,2),auxmat(1,1))
call matvec2(auxmat(1,1),Ub2(1,i+4),vtemp3(1))
call matmat2(achuj_temp(1,1),EUg(1,1,i+2),gtemp(1,1))
call matmat2(gtemp(1,1),EUg(1,1,i+3),gtemp(1,1))
call matvec2(a_chuj(1,1,jj,i),Ub2(1,i+4),vtemp4(1))
- ss13 = scalar2(b1(1,itk),vtemp4(1))
+ ss13 = scalar2(b1(1,k),vtemp4(1))
s13 = (gtemp(1,1)+gtemp(2,2))*ss13
#endif
c write (2,*) 's1,s2,s8,s12,s13',s1,s2,s8,s12,s13
s1d = (auxmatd(1,1)+auxmatd(2,2))*ss1
call transpose2(AEAderg(1,1,2),atempd(1,1))
call matmat2(atempd(1,1),EUg(1,1,i+4),atempd(1,1))
- s8d = -(atempd(1,1)+atempd(2,2))*scalar2(cc(1,1,itl),vtemp2(1))
+ s8d = -(atempd(1,1)+atempd(2,2))*scalar2(cc(1,1,l),vtemp2(1))
#endif
call matmat2(EUg(1,1,i+3),AEAderg(1,1,2),auxmatd(1,1))
call matvec2(auxmatd(1,1),Ub2(1,i+4),vtemp3d(1))
#ifdef MOMENT
call transpose2(AEA(1,1,1),auxmatd(1,1))
call matmat2(EUg(1,1,i+1),auxmatd(1,1),auxmatd(1,1))
- ss1d=scalar2(Ub2der(1,i+2),b1(1,itl))
+ ss1d=scalar2(Ub2der(1,i+2),b1(1,l))
s1d = (auxmatd(1,1)+auxmatd(2,2))*ss1d
#endif
- call matvec2(EUgder(1,1,i+2),b1(1,itl),vtemp1d(1))
+ call matvec2(EUgder(1,1,i+2),b1(1,l),vtemp1d(1))
call matvec2(AEA(1,1,1),vtemp1d(1),vtemp1d(1))
- s2d = scalar2(b1(1,itk),vtemp1d(1))
+ s2d = scalar2(b1(1,k),vtemp1d(1))
#ifdef MOMENT
- call matvec2(Ug2der(1,1,i+2),dd(1,1,itk1),vtemp2d(1))
- s8d = -(atemp(1,1)+atemp(2,2))*scalar2(cc(1,1,itl),vtemp2d(1))
+ call matvec2(Ug2der(1,1,i+2),dd(1,1,k+1),vtemp2d(1))
+ s8d = -(atemp(1,1)+atemp(2,2))*scalar2(cc(1,1,l),vtemp2d(1))
#endif
s12d = scalar2(Ub2der(1,i+2),vtemp3(1))
#ifdef MOMENT
call matmat2(EUg(1,1,i+1),auxmatd(1,1),auxmatd(1,1))
s1d = (auxmatd(1,1)+auxmatd(2,2))*ss1
#endif
- call matvec2(EUg(1,1,i+2),b1(1,itl),vtemp1d(1))
+ call matvec2(EUg(1,1,i+2),b1(1,l),vtemp1d(1))
call matvec2(AEAderg(1,1,1),vtemp1d(1),vtemp1d(1))
- s2d = scalar2(b1(1,itk),vtemp1d(1))
+ s2d = scalar2(b1(1,k),vtemp1d(1))
#ifdef MOMENT
call transpose2(AEA(1,1,2),atempd(1,1))
call matmat2(atempd(1,1),EUgder(1,1,i+4),atempd(1,1))
- s8d = -(atempd(1,1)+atempd(2,2))*scalar2(cc(1,1,itl),vtemp2(1))
+ s8d = -(atempd(1,1)+atempd(2,2))*scalar2(cc(1,1,l),vtemp2(1))
#endif
call matvec2(auxmat(1,1),Ub2der(1,i+4),vtemp3d(1))
s12d = scalar2(Ub2(1,i+2),vtemp3d(1))
#ifdef MOMENT
call matvec2(a_chuj(1,1,jj,i),Ub2der(1,i+4),vtemp4d(1))
- ss13d = scalar2(b1(1,itk),vtemp4d(1))
+ ss13d = scalar2(b1(1,k),vtemp4d(1))
s13d = (gtemp(1,1)+gtemp(2,2))*ss13d
#endif
c s1d=0.0d0
call matmat2(EUg(1,1,i+1),auxmatd(1,1),auxmatd(1,1))
s1d = (auxmatd(1,1)+auxmatd(2,2))*ss1
#endif
- call matvec2(EUg(1,1,i+2),b1(1,itl),vtemp1(1))
+ call matvec2(EUg(1,1,i+2),b1(1,l),vtemp1(1))
call matvec2(AEAderx(1,1,lll,kkk,iii,1),vtemp1(1),
& vtemp1d(1))
- s2d = scalar2(b1(1,itk),vtemp1d(1))
+ s2d = scalar2(b1(1,k),vtemp1d(1))
#ifdef MOMENT
call transpose2(AEAderx(1,1,lll,kkk,iii,2),atempd(1,1))
call matmat2(atempd(1,1),EUg(1,1,i+4),atempd(1,1))
s8d = -(atempd(1,1)+atempd(2,2))*
- & scalar2(cc(1,1,itl),vtemp2(1))
+ & scalar2(cc(1,1,l),vtemp2(1))
#endif
call matmat2(EUg(1,1,i+3),AEAderx(1,1,lll,kkk,iii,2),
& auxmatd(1,1))
derx_turn(lll,kkk,2) = derx_turn(lll,kkk,2)-0.5d0*s13d
call matvec2(a_chuj_der(1,1,lll,kkk,jj,i),Ub2(1,i+4),
& vtemp4d(1))
- ss13d = scalar2(b1(1,itk),vtemp4d(1))
+ ss13d = scalar2(b1(1,k),vtemp4d(1))
s13d = (gtemp(1,1)+gtemp(2,2))*ss13d
derx_turn(lll,kkk,1) = derx_turn(lll,kkk,1)-0.5d0*s13d
enddo
return
end
+CCC----------------------------------------------
+ subroutine Eliptransfer(eliptran)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.LOCAL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.NAMES'
+ include 'COMMON.INTERACT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CALC'
+ include 'COMMON.CONTROL'
+ include 'COMMON.SPLITELE'
+ include 'COMMON.SBRIDGE'
+C this is done by Adasko
+C print *,"wchodze"
+C structure of box:
+C water
+C--bordliptop-- buffore starts
+C--bufliptop--- here true lipid starts
+C lipid
+C--buflipbot--- lipid ends buffore starts
+C--bordlipbot--buffore ends
+ eliptran=0.0
+ do i=ilip_start,ilip_end
+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.0.0) positi=positi+boxzsize
+C print *,i
+C first for peptide groups
+c for each residue check if it is in lipid or lipid water border area
+ if ((positi.gt.bordlipbot)
+ &.and.(positi.lt.bordliptop)) then
+C the energy transfer exist
+ if (positi.lt.buflipbot) then
+C what fraction I am in
+ fracinbuf=1.0d0-
+ & ((positi-bordlipbot)/lipbufthick)
+C lipbufthick is thickenes of lipid buffore
+ sslip=sscalelip(fracinbuf)
+ ssgradlip=-sscagradlip(fracinbuf)/lipbufthick
+ eliptran=eliptran+sslip*pepliptran
+ gliptranc(3,i)=gliptranc(3,i)+ssgradlip*pepliptran/2.0d0
+ gliptranc(3,i-1)=gliptranc(3,i-1)+ssgradlip*pepliptran/2.0d0
+C gliptranc(3,i-2)=gliptranc(3,i)+ssgradlip*pepliptran
+
+C print *,"doing sccale for lower part"
+C print *,i,sslip,fracinbuf,ssgradlip
+ elseif (positi.gt.bufliptop) then
+ fracinbuf=1.0d0-((bordliptop-positi)/lipbufthick)
+ sslip=sscalelip(fracinbuf)
+ ssgradlip=sscagradlip(fracinbuf)/lipbufthick
+ eliptran=eliptran+sslip*pepliptran
+ gliptranc(3,i)=gliptranc(3,i)+ssgradlip*pepliptran/2.0d0
+ gliptranc(3,i-1)=gliptranc(3,i-1)+ssgradlip*pepliptran/2.0d0
+C gliptranc(3,i-2)=gliptranc(3,i)+ssgradlip*pepliptran
+C print *, "doing sscalefor top part"
+C print *,i,sslip,fracinbuf,ssgradlip
+ else
+ eliptran=eliptran+pepliptran
+C print *,"I am in true lipid"
+ endif
+C else
+C eliptran=elpitran+0.0 ! I am in water
+ endif
+ enddo
+C print *, "nic nie bylo w lipidzie?"
+C now multiply all by the peptide group transfer factor
+C eliptran=eliptran*pepliptran
+C now the same for side chains
+CV do i=1,1
+ do i=ilip_start,ilip_end
+ if (itype(i).eq.ntyp1) cycle
+ positi=(mod(c(3,i+nres),boxzsize))
+ if (positi.le.0) positi=positi+boxzsize
+C print *,mod(c(3,i+nres),boxzsize),bordlipbot,bordliptop
+c for each residue check if it is in lipid or lipid water border area
+C respos=mod(c(3,i+nres),boxzsize)
+C print *,positi,bordlipbot,buflipbot
+ if ((positi.gt.bordlipbot)
+ & .and.(positi.lt.bordliptop)) then
+C the energy transfer exist
+ if (positi.lt.buflipbot) then
+ fracinbuf=1.0d0-
+ & ((positi-bordlipbot)/lipbufthick)
+C lipbufthick is thickenes of lipid buffore
+ sslip=sscalelip(fracinbuf)
+ ssgradlip=-sscagradlip(fracinbuf)/lipbufthick
+ eliptran=eliptran+sslip*liptranene(itype(i))
+ gliptranx(3,i)=gliptranx(3,i)
+ &+ssgradlip*liptranene(itype(i))
+ gliptranc(3,i-1)= gliptranc(3,i-1)
+ &+ssgradlip*liptranene(itype(i))
+C print *,"doing sccale for lower part"
+ elseif (positi.gt.bufliptop) then
+ fracinbuf=1.0d0-
+ &((bordliptop-positi)/lipbufthick)
+ sslip=sscalelip(fracinbuf)
+ ssgradlip=sscagradlip(fracinbuf)/lipbufthick
+ eliptran=eliptran+sslip*liptranene(itype(i))
+ gliptranx(3,i)=gliptranx(3,i)
+ &+ssgradlip*liptranene(itype(i))
+ gliptranc(3,i-1)= gliptranc(3,i-1)
+ &+ssgradlip*liptranene(itype(i))
+C print *, "doing sscalefor top part",sslip,fracinbuf
+ else
+ eliptran=eliptran+liptranene(itype(i))
+C print *,"I am in true lipid"
+ endif
+ endif ! if in lipid or buffor
+C else
+C eliptran=elpitran+0.0 ! I am in water
+ enddo
+ return
+ end
+C---------------------------------------------------------
+C AFM soubroutine for constant force
+ subroutine AFMforce(Eafmforce)
+ 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'
+ real*8 diffafm(3)
+ dist=0.0d0
+ Eafmforce=0.0d0
+ do i=1,3
+ diffafm(i)=c(i,afmend)-c(i,afmbeg)
+ dist=dist+diffafm(i)**2
+ enddo
+ dist=dsqrt(dist)
+ Eafmforce=-forceAFMconst*(dist-distafminit)
+ do i=1,3
+ gradafm(i,afmend-1)=-forceAFMconst*diffafm(i)/dist
+ gradafm(i,afmbeg-1)=forceAFMconst*diffafm(i)/dist
+ enddo
+C print *,'AFM',Eafmforce
+ return
+ end
+C---------------------------------------------------------
+C AFM subroutine with pseudoconstant velocity
+ subroutine AFMvel(Eafmforce)
+ 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'
+ real*8 diffafm(3)
+C Only for check grad COMMENT if not used for checkgrad
+C totT=3.0d0
+C--------------------------------------------------------
+C print *,"wchodze"
+ dist=0.0d0
+ Eafmforce=0.0d0
+ do i=1,3
+ diffafm(i)=c(i,afmend)-c(i,afmbeg)
+ dist=dist+diffafm(i)**2
+ enddo
+ dist=dsqrt(dist)
+ Eafmforce=0.5d0*forceAFMconst
+ & *(distafminit+totTafm*velAFMconst-dist)**2
+C Eafmforce=-forceAFMconst*(dist-distafminit)
+ do i=1,3
+ gradafm(i,afmend-1)=-forceAFMconst*
+ &(distafminit+totTafm*velAFMconst-dist)
+ &*diffafm(i)/dist
+ gradafm(i,afmbeg-1)=forceAFMconst*
+ &(distafminit+totTafm*velAFMconst-dist)
+ &*diffafm(i)/dist
+ enddo
+C print *,'AFM',Eafmforce,totTafm*velAFMconst,dist
+ return
+ end
+C-----------------------------------------------------------
+C first for shielding is setting of function of side-chains
+ subroutine set_shield_fac
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.SHIELD'
+ include 'COMMON.INTERACT'
+C this is the squar root 77 devided by 81 the epislion in lipid (in protein)
+ double precision div77_81/0.974996043d0/,
+ &div4_81/0.2222222222d0/,sh_frac_dist_grad(3)
+
+C the vector between center of side_chain and peptide group
+ double precision pep_side(3),long,side_calf(3),
+ &pept_group(3),costhet_grad(3),cosphi_grad_long(3),
+ &cosphi_grad_loc(3),pep_side_norm(3),side_calf_norm(3)
+C the line belowe needs to be changed for FGPROC>1
+ do i=1,nres-1
+ if ((itype(i).eq.ntyp1).and.itype(i+1).eq.ntyp1) cycle
+ ishield_list(i)=0
+Cif there two consequtive dummy atoms there is no peptide group between them
+C the line below has to be changed for FGPROC>1
+ VolumeTotal=0.0
+ do k=1,nres
+ if ((itype(k).eq.ntyp1).or.(itype(k).eq.10)) cycle
+ dist_pep_side=0.0
+ dist_side_calf=0.0
+ do j=1,3
+C first lets set vector conecting the ithe side-chain with kth side-chain
+ pep_side(j)=c(j,k+nres)-(c(j,i)+c(j,i+1))/2.0d0
+C pep_side(j)=2.0d0
+C and vector conecting the side-chain with its proper calfa
+ side_calf(j)=c(j,k+nres)-c(j,k)
+C side_calf(j)=2.0d0
+ pept_group(j)=c(j,i)-c(j,i+1)
+C lets have their lenght
+ dist_pep_side=pep_side(j)**2+dist_pep_side
+ dist_side_calf=dist_side_calf+side_calf(j)**2
+ dist_pept_group=dist_pept_group+pept_group(j)**2
+ enddo
+ dist_pep_side=dsqrt(dist_pep_side)
+ dist_pept_group=dsqrt(dist_pept_group)
+ dist_side_calf=dsqrt(dist_side_calf)
+ do j=1,3
+ pep_side_norm(j)=pep_side(j)/dist_pep_side
+ side_calf_norm(j)=dist_side_calf
+ enddo
+C now sscale fraction
+ sh_frac_dist=-(dist_pep_side-rpp(1,1)-buff_shield)/buff_shield
+C print *,buff_shield,"buff"
+C now sscale
+ if (sh_frac_dist.le.0.0) cycle
+C If we reach here it means that this side chain reaches the shielding sphere
+C Lets add him to the list for gradient
+ ishield_list(i)=ishield_list(i)+1
+C ishield_list is a list of non 0 side-chain that contribute to factor gradient
+C this list is essential otherwise problem would be O3
+ shield_list(ishield_list(i),i)=k
+C Lets have the sscale value
+ if (sh_frac_dist.gt.1.0) then
+ scale_fac_dist=1.0d0
+ do j=1,3
+ sh_frac_dist_grad(j)=0.0d0
+ enddo
+ else
+ scale_fac_dist=-sh_frac_dist*sh_frac_dist
+ & *(2.0*sh_frac_dist-3.0d0)
+ fac_help_scale=6.0*(sh_frac_dist-sh_frac_dist**2)
+ & /dist_pep_side/buff_shield*0.5
+C remember for the final gradient multiply sh_frac_dist_grad(j)
+C for side_chain by factor -2 !
+ do j=1,3
+ sh_frac_dist_grad(j)=fac_help_scale*pep_side(j)
+C print *,"jestem",scale_fac_dist,fac_help_scale,
+C & sh_frac_dist_grad(j)
+ enddo
+ endif
+C if ((i.eq.3).and.(k.eq.2)) then
+C print *,i,sh_frac_dist,dist_pep,fac_help_scale,scale_fac_dist
+C & ,"TU"
+C endif
+
+C this is what is now we have the distance scaling now volume...
+ short=short_r_sidechain(itype(k))
+ long=long_r_sidechain(itype(k))
+ costhet=1.0d0/dsqrt(1.0+short**2/dist_pep_side**2)
+C now costhet_grad
+C costhet=0.0d0
+ costhet_fac=costhet**3*short**2*(-0.5)/dist_pep_side**4
+C costhet_fac=0.0d0
+ do j=1,3
+ costhet_grad(j)=costhet_fac*pep_side(j)
+ enddo
+C remember for the final gradient multiply costhet_grad(j)
+C for side_chain by factor -2 !
+C fac alfa is angle between CB_k,CA_k, CA_i,CA_i+1
+C pep_side0pept_group is vector multiplication
+ pep_side0pept_group=0.0
+ do j=1,3
+ pep_side0pept_group=pep_side0pept_group+pep_side(j)*side_calf(j)
+ enddo
+ cosalfa=(pep_side0pept_group/
+ & (dist_pep_side*dist_side_calf))
+ fac_alfa_sin=1.0-cosalfa**2
+ fac_alfa_sin=dsqrt(fac_alfa_sin)
+ rkprim=fac_alfa_sin*(long-short)+short
+C now costhet_grad
+ cosphi=1.0d0/dsqrt(1.0+rkprim**2/dist_pep_side**2)
+ cosphi_fac=cosphi**3*rkprim**2*(-0.5)/dist_pep_side**4
+
+ do j=1,3
+ cosphi_grad_long(j)=cosphi_fac*pep_side(j)
+ &+cosphi**3*0.5/dist_pep_side**2*(-rkprim)
+ &*(long-short)/fac_alfa_sin*cosalfa/
+ &((dist_pep_side*dist_side_calf))*
+ &((side_calf(j))-cosalfa*
+ &((pep_side(j)/dist_pep_side)*dist_side_calf))
+
+ cosphi_grad_loc(j)=cosphi**3*0.5/dist_pep_side**2*(-rkprim)
+ &*(long-short)/fac_alfa_sin*cosalfa
+ &/((dist_pep_side*dist_side_calf))*
+ &(pep_side(j)-
+ &cosalfa*side_calf(j)/dist_side_calf*dist_pep_side)
+ enddo
+
+ VofOverlap=VSolvSphere/2.0d0*(1.0-costhet)*(1.0-cosphi)
+ & /VSolvSphere_div
+ & *wshield
+C now the gradient...
+C grad_shield is gradient of Calfa for peptide groups
+C write(iout,*) "shield_compon",i,k,VSolvSphere,scale_fac_dist,
+C & costhet,cosphi
+C write(iout,*) "cosphi_compon",i,k,pep_side0pept_group,
+C & dist_pep_side,dist_side_calf,c(1,k+nres),c(1,k),itype(k)
+ do j=1,3
+ grad_shield(j,i)=grad_shield(j,i)
+C gradient po skalowaniu
+ & +(sh_frac_dist_grad(j)
+C gradient po costhet
+ &-scale_fac_dist*costhet_grad(j)/(1.0-costhet)
+ &-scale_fac_dist*(cosphi_grad_long(j))
+ &/(1.0-cosphi) )*div77_81
+ &*VofOverlap
+C grad_shield_side is Cbeta sidechain gradient
+ grad_shield_side(j,ishield_list(i),i)=
+ & (sh_frac_dist_grad(j)*(-2.0d0)
+ & +scale_fac_dist*costhet_grad(j)*2.0d0/(1.0-costhet)
+ & +scale_fac_dist*(cosphi_grad_long(j))
+ & *2.0d0/(1.0-cosphi))
+ & *div77_81*VofOverlap
+
+ grad_shield_loc(j,ishield_list(i),i)=
+ & scale_fac_dist*cosphi_grad_loc(j)
+ & *2.0d0/(1.0-cosphi)
+ & *div77_81*VofOverlap
+ enddo
+ VolumeTotal=VolumeTotal+VofOverlap*scale_fac_dist
+ enddo
+ fac_shield(i)=VolumeTotal*div77_81+div4_81
+c write(2,*) "TOTAL VOLUME",i,VolumeTotal,fac_shield(i)
+ enddo
+ return
+ end
+C--------------------------------------------------------------------------
+ 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'
+C this is the squar root 77 devided by 81 the epislion in lipid (in protein)
+ double precision div77_81/0.974996043d0/,
+ &div4_81/0.2222222222d0/,sh_frac_dist_grad(3)
+
+C the vector between center of side_chain and peptide group
+ double precision pep_side(3),long,side_calf(3),
+ &pept_group(3),costhet_grad(3),cosphi_grad_long(3),
+ &cosphi_grad_loc(3),pep_side_norm(3),side_calf_norm(3)
+C the line belowe needs to be changed for FGPROC>1
+ do i=1,nres-1
+ if ((itype(i).eq.ntyp1).and.itype(i+1).eq.ntyp1) cycle
+ ishield_list(i)=0
+Cif there two consequtive dummy atoms there is no peptide group between them
+C the line below has to be changed for FGPROC>1
+ VolumeTotal=0.0
+ do k=1,nres
+ if ((itype(k).eq.ntyp1).or.(itype(k).eq.10)) cycle
+ dist_pep_side=0.0
+ dist_side_calf=0.0
+ do j=1,3
+C first lets set vector conecting the ithe side-chain with kth side-chain
+ pep_side(j)=c(j,k+nres)-(c(j,i)+c(j,i+1))/2.0d0
+C pep_side(j)=2.0d0
+C and vector conecting the side-chain with its proper calfa
+ side_calf(j)=c(j,k+nres)-c(j,k)
+C side_calf(j)=2.0d0
+ pept_group(j)=c(j,i)-c(j,i+1)
+C lets have their lenght
+ dist_pep_side=pep_side(j)**2+dist_pep_side
+ dist_side_calf=dist_side_calf+side_calf(j)**2
+ dist_pept_group=dist_pept_group+pept_group(j)**2
+ enddo
+ dist_pep_side=dsqrt(dist_pep_side)
+ dist_pept_group=dsqrt(dist_pept_group)
+ dist_side_calf=dsqrt(dist_side_calf)
+ do j=1,3
+ pep_side_norm(j)=pep_side(j)/dist_pep_side
+ side_calf_norm(j)=dist_side_calf
+ enddo
+C now sscale fraction
+ sh_frac_dist=-(dist_pep_side-rpp(1,1)-buff_shield)/buff_shield
+C print *,buff_shield,"buff"
+C now sscale
+ if (sh_frac_dist.le.0.0) cycle
+C If we reach here it means that this side chain reaches the shielding sphere
+C Lets add him to the list for gradient
+ ishield_list(i)=ishield_list(i)+1
+C ishield_list is a list of non 0 side-chain that contribute to factor gradient
+C this list is essential otherwise problem would be O3
+ shield_list(ishield_list(i),i)=k
+C Lets have the sscale value
+ if (sh_frac_dist.gt.1.0) then
+ scale_fac_dist=1.0d0
+ do j=1,3
+ sh_frac_dist_grad(j)=0.0d0
+ enddo
+ else
+ scale_fac_dist=-sh_frac_dist*sh_frac_dist
+ & *(2.0d0*sh_frac_dist-3.0d0)
+ fac_help_scale=6.0d0*(sh_frac_dist-sh_frac_dist**2)
+ & /dist_pep_side/buff_shield*0.5d0
+C remember for the final gradient multiply sh_frac_dist_grad(j)
+C for side_chain by factor -2 !
+ do j=1,3
+ sh_frac_dist_grad(j)=fac_help_scale*pep_side(j)
+C sh_frac_dist_grad(j)=0.0d0
+C scale_fac_dist=1.0d0
+C print *,"jestem",scale_fac_dist,fac_help_scale,
+C & sh_frac_dist_grad(j)
+ enddo
+ endif
+C this is what is now we have the distance scaling now volume...
+ short=short_r_sidechain(itype(k))
+ long=long_r_sidechain(itype(k))
+ costhet=1.0d0/dsqrt(1.0d0+short**2/dist_pep_side**2)
+ sinthet=short/dist_pep_side*costhet
+C now costhet_grad
+C costhet=0.6d0
+C sinthet=0.8
+ costhet_fac=costhet**3*short**2*(-0.5d0)/dist_pep_side**4
+C sinthet_fac=costhet**2*0.5d0*(short**3/dist_pep_side**4*costhet
+C & -short/dist_pep_side**2/costhet)
+C costhet_fac=0.0d0
+ do j=1,3
+ costhet_grad(j)=costhet_fac*pep_side(j)
+ enddo
+C remember for the final gradient multiply costhet_grad(j)
+C for side_chain by factor -2 !
+C fac alfa is angle between CB_k,CA_k, CA_i,CA_i+1
+C pep_side0pept_group is vector multiplication
+ pep_side0pept_group=0.0d0
+ do j=1,3
+ pep_side0pept_group=pep_side0pept_group+pep_side(j)*side_calf(j)
+ enddo
+ cosalfa=(pep_side0pept_group/
+ & (dist_pep_side*dist_side_calf))
+ fac_alfa_sin=1.0d0-cosalfa**2
+ fac_alfa_sin=dsqrt(fac_alfa_sin)
+ rkprim=fac_alfa_sin*(long-short)+short
+C rkprim=short
+
+C now costhet_grad
+ cosphi=1.0d0/dsqrt(1.0d0+rkprim**2/dist_pep_side**2)
+C cosphi=0.6
+ cosphi_fac=cosphi**3*rkprim**2*(-0.5d0)/dist_pep_side**4
+ sinphi=rkprim/dist_pep_side/dsqrt(1.0d0+rkprim**2/
+ & dist_pep_side**2)
+C sinphi=0.8
+ do j=1,3
+ cosphi_grad_long(j)=cosphi_fac*pep_side(j)
+ &+cosphi**3*0.5d0/dist_pep_side**2*(-rkprim)
+ &*(long-short)/fac_alfa_sin*cosalfa/
+ &((dist_pep_side*dist_side_calf))*
+ &((side_calf(j))-cosalfa*
+ &((pep_side(j)/dist_pep_side)*dist_side_calf))
+C cosphi_grad_long(j)=0.0d0
+ cosphi_grad_loc(j)=cosphi**3*0.5d0/dist_pep_side**2*(-rkprim)
+ &*(long-short)/fac_alfa_sin*cosalfa
+ &/((dist_pep_side*dist_side_calf))*
+ &(pep_side(j)-
+ &cosalfa*side_calf(j)/dist_side_calf*dist_pep_side)
+C cosphi_grad_loc(j)=0.0d0
+ enddo
+C print *,sinphi,sinthet
+c write (iout,*) "VSolvSphere",VSolvSphere," VSolvSphere_div",
+c & VSolvSphere_div," sinphi",sinphi," sinthet",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
+c write (iout,*) "VofOverlap",VofOverlap," scale_fac_dist",
+c & scale_fac_dist
+ VolumeTotal=VolumeTotal+VofOverlap*scale_fac_dist
+ enddo
+ fac_shield(i)=VolumeTotal*wshield+(1.0d0-wshield)
+c write(2,*) "TOTAL VOLUME",i,VolumeTotal,fac_shield(i),
+c & " wshield",wshield
+c write(2,*) "TU",rpp(1,1),short,long,buff_shield
+ 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=1,2*nres
+ enetube(i)=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=1,nres
+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
+ vectube(1)=mod((c(1,i)+c(1,i+1))/2.0d0,boxxsize)
+ if (vectube(1).lt.0) vectube(1)=vectube(1)+boxxsize
+ vectube(2)=mod((c(2,i)+c(2,i+1))/2.0d0,boxxsize)
+ if (vectube(2).lt.0) vectube(2)=vectube(2)+boxxsize
+ 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)
+ do i=1,nres
+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
+ 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),boxxsize)
+ if (vectube(2).lt.0) vectube(2)=vectube(2)+boxxsize
+
+ 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=1,2*nres
+ Etube=Etube+enetube(i)
+ 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=1,2*nres
+ enetube(i)=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=1,nres
+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
+ vectube(1)=mod((c(1,i)+c(1,i+1))/2.0d0,boxxsize)
+ if (vectube(1).lt.0) vectube(1)=vectube(1)+boxxsize
+ vectube(2)=mod((c(2,i)+c(2,i+1))/2.0d0,boxxsize)
+ if (vectube(2).lt.0) vectube(2)=vectube(2)+boxxsize
+ 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)
+ do i=1,nres
+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),boxxsize)
+ if (vectube(2).lt.0) vectube(2)=vectube(2)+boxxsize
+
+ 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))
+ gg_tube_SC(3,i)=gg_tube_SC(3,i)
+ &+ssgradtube*tubetranene(itype(i))
+ gg_tube(3,i-1)= gg_tube(3,i-1)
+ &+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=1,2*nres
+ Etube=Etube+enetube(i)
+ 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
projects / unres.git / blobdiff