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)
#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
C Calculate the virtual-bond-angle energy.
C
if (wang.gt.0d0) then
- call ebend(ebe)
+ if ((tor_mode.eq.0).or.(tor_mode.eq.2)) then
+ call ebend(ebe,ethetacnstr)
+ endif
+C ebend kcc is Kubo cumulant clustered rigorous attemp to derive the
+C energy function
+ if ((tor_mode.eq.1).or.(tor_mode.eq.2)) then
+ call ebend_kcc(ebe,ethetacnstr)
+ endif
else
ebe=0
+ ethetacnstr=0
endif
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
+C print *,"tor",tor_mode
if (wtor.gt.0) then
+ if ((tor_mode.eq.0).or.(tor_mode.eq.2)) then
call etor(etors,edihcnstr)
+ endif
+C etor kcc is Kubo cumulant clustered rigorous attemp to derive the
+C energy function
+ if ((tor_mode.eq.1).or.(tor_mode.eq.2)) then
+ call etor_kcc(etors,edihcnstr)
+ endif
else
etors=0
edihcnstr=0
C
C 6/23/01 Calculate double-torsional energy
C
- if (wtor_d.gt.0) then
+ if ((wtor_d.gt.0).and.((tor_mode.eq.0).or.(tor_mode.eq.2))) then
call etor_d(etors_d)
else
etors_d=0
else
esccor=0.0d0
endif
+C print *,"PRZED MULIt"
c print *,"Processor",myrank," computed Usccorr"
C
C 12/1/95 Multi-body terms
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.gt.0) then
+C print *,"just before call"
+ call calctube(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"
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+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+Uconst+wsccor*esccor+wliptran*eliptran
+ & +Eafmforce
+ & +ethetacnstr+wtube*Etube
#endif
energia(0)=etot
c detecting NaNQ
#ifdef MPI
include 'mpif.h'
#endif
- double precision gradbufc(3,maxres),gradbufx(3,maxres),
- & glocbuf(4*maxres),gradbufc_sum(3,maxres),gloc_scbuf(3,maxres)
+ 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'
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
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
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,*)'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
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)
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.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.
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
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=iabs(itype(j))
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
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*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=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
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
+ 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
+
dxi=dc_norm(1,nres+i)
dyi=dc_norm(2,nres+i)
dzi=dc_norm(3,nres+i)
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=mod(xj,boxxsize)
+ if (xj.lt.0) xj=xj+boxxsize
+ yj=mod(yj,boxysize)
+ if (yj.lt.0) yj=yj+boxysize
+ zj=mod(zj,boxzsize)
+ if (zj.lt.0) zj=zj+boxzsize
+ if ((zj.gt.bordlipbot)
+ &.and.(zj.lt.bordliptop)) then
+C the energy transfer exist
+ if (zj.lt.buflipbot) then
+C what fraction I am in
+ fracinbuf=1.0d0-
+ & ((zj-bordlipbot)/lipbufthick)
+C lipbufthick is thickenes of lipid buffore
+ sslipj=sscalelip(fracinbuf)
+ ssgradlipj=-sscagradlip(fracinbuf)/lipbufthick
+ elseif (zj.gt.bufliptop) then
+ fracinbuf=1.0d0-((bordliptop-zj)/lipbufthick)
+ sslipj=sscalelip(fracinbuf)
+ ssgradlipj=sscagradlip(fracinbuf)/lipbufthick
+ else
+ sslipj=1.0d0
+ ssgradlipj=0.0
+ endif
+ else
+ sslipj=0.0d0
+ ssgradlipj=0.0
+ endif
+ aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0
+ & +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+ bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0
+ & +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+C if (aa.ne.aa_aq(itypi,itypj)) write(63,'2e10.5')
+C &(aa-aa_aq(itypi,itypj)),(bb-bb_aq(itypi,itypj))
+C write(iout,*) "tu,", i,j,aa,bb,aa_lip(itypi,itypj),sslipi,sslipj
+ dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
+ xj_safe=xj
+ yj_safe=yj
+ 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---------------------------------------------------------------
rij_shift=1.0D0/rij_shift
fac=rij_shift**expon
- e1=fac*fac*aa(itypi,itypj)
- e2=fac*bb(itypi,itypj)
+ e1=fac*fac*aa
+ e2=fac*bb
evdwij=eps1*eps2rt*eps3rt*(e1+e2)
eps2der=evdwij*eps3rt
eps3der=evdwij*eps2rt
evdwij=evdwij*eps2rt*eps3rt
evdw=evdw+evdwij+e_augm
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
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*sss
- gvdwx(k,j)=gvdwx(k,j)+gg(k)
+ 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*sss
c write (iout,*)(eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i))
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
#endif
#ifdef NEWCORR
if (i.gt. nnt+2 .and. i.lt.nct+2) then
- iti = itortyp(itype(i-2))
+ iti = itype2loc(itype(i-2))
else
- iti=ntortyp+1
+ iti=nloctyp
endif
c if (i.gt. iatel_s+1 .and. i.lt.iatel_e+4) then
if (i.gt. nnt+1 .and. i.lt.nct+1) then
- iti1 = itortyp(itype(i-1))
+ iti1 = itype2loc(itype(i-1))
else
- iti1=ntortyp+1
+ iti1=nloctyp
endif
c write(iout,*),i
- b1(1,i-2)=bnew1(1,1,iti)*dsin(theta(i-1)/2.0)
+ b1(1,i-2)=bnew1(1,1,iti)*dsin(theta(i-1)/2.0d0)
& +bnew1(2,1,iti)*dsin(theta(i-1))
- & +bnew1(3,1,iti)*dcos(theta(i-1)/2.0)
+ & +bnew1(3,1,iti)*dcos(theta(i-1)/2.0d0)
gtb1(1,i-2)=bnew1(1,1,iti)*dcos(theta(i-1)/2.0d0)/2.0d0
& +bnew1(2,1,iti)*dcos(theta(i-1))
& -bnew1(3,1,iti)*dsin(theta(i-1)/2.0d0)/2.0d0
c & +bnew1(3,1,iti)*sin(alpha(i))*cos(beta(i))
c &*(cos(theta(i)/2.0)
- b2(1,i-2)=bnew2(1,1,iti)*dsin(theta(i-1)/2.0)
+ b2(1,i-2)=bnew2(1,1,iti)*dsin(theta(i-1)/2.0d0)
& +bnew2(2,1,iti)*dsin(theta(i-1))
- & +bnew2(3,1,iti)*dcos(theta(i-1)/2.0)
+ & +bnew2(3,1,iti)*dcos(theta(i-1)/2.0d0)
c & +bnew2(3,1,iti)*sin(alpha(i))*cos(beta(i))
c &*(cos(theta(i)/2.0)
gtb2(1,i-2)=bnew2(1,1,iti)*dcos(theta(i-1)/2.0d0)/2.0d0
c write(iout,*) 'b1=',b1(1,i-2)
c write (iout,*) 'theta=', theta(i-1)
enddo
+#else
+ if (i.gt. nnt+2 .and. i.lt.nct+2) then
+ iti = itype2loc(itype(i-2))
+ else
+ iti=nloctyp
+ endif
+c if (i.gt. iatel_s+1 .and. i.lt.iatel_e+4) then
+ if (i.gt. nnt+1 .and. i.lt.nct+1) then
+ iti1 = itype2loc(itype(i-1))
+ else
+ iti1=nloctyp
+ endif
+ b1(1,i-2)=b(3,iti)
+ b1(2,i-2)=b(5,iti)
+ b2(1,i-2)=b(2,iti)
+ b2(2,i-2)=b(4,iti)
+ 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)
+ EE(1,2,i-2)=eeold(1,2,iti)
+ EE(2,1,i-2)=eeold(2,1,iti)
+ EE(2,2,i-2)=eeold(2,2,iti)
+ EE(1,1,i-2)=eeold(1,1,iti)
+ enddo
+#endif
#ifdef PARMAT
do i=ivec_start+2,ivec_end+2
#else
do i=3,nres+1
#endif
-#endif
if (i .lt. nres+1) then
sin1=dsin(phi(i))
cos1=dcos(phi(i))
endif
c if (i.gt. iatel_s+2 .and. i.lt.iatel_e+5) then
if (i.gt. nnt+2 .and. i.lt.nct+2) then
- iti = itortyp(itype(i-2))
+ iti = itype2loc(itype(i-2))
else
- iti=ntortyp
+ iti=nloctyp
endif
c if (i.gt. iatel_s+1 .and. i.lt.iatel_e+4) then
if (i.gt. nnt+1 .and. i.lt.nct+1) then
- iti1 = itortyp(itype(i-1))
+ iti1 = itype2loc(itype(i-1))
else
- iti1=ntortyp
+ iti1=nloctyp
endif
cd write (iout,*) '*******i',i,' iti1',iti
cd write (iout,*) 'b1',b1(:,iti)
call matvec2(Ug(1,1,i-2),gtb2(1,i-2),gUb2(1,i-2))
c write (iout,*) Ug(1,1,i-2),gtb2(1,i-2),gUb2(1,i-2),"chuj"
#endif
-c write(iout,*) "co jest kurwa", iti, EE(1,1,iti),EE(2,1,iti),
-c & EE(1,2,iti),EE(2,2,iti)
+c write(iout,*) "co jest kurwa", iti, EE(1,1,i),EE(2,1,i),
+c & EE(1,2,iti),EE(2,2,i)
call matmat2(EE(1,1,i-2),Ug(1,1,i-2),EUg(1,1,i-2))
call matmat2(gtEE(1,1,i-2),Ug(1,1,i-2),gtEUg(1,1,i-2))
c write(iout,*) "Macierz EUG",
c if (i.gt. iatel_s+1 .and. i.lt.iatel_e+4) then
if (i.gt. nnt+1 .and. i.lt.nct+1) then
if (itype(i-1).le.ntyp) then
- iti1 = itortyp(itype(i-1))
+ iti1 = itype2loc(itype(i-1))
else
- iti1=ntortyp
+ iti1=nloctyp
endif
else
- iti1=ntortyp
+ iti1=nloctyp
endif
do k=1,2
mu(k,i-2)=Ub2(k,i-2)+b1(k,i-1)
enddo
-c write (iout,*) 'mu ',mu(:,i-2),i-2
+#ifdef MUOUT
+ write (iout,'(2hmu,i3,3f8.1,12f10.5)') i-2,rad2deg*theta(i-1),
+ & rad2deg*theta(i),rad2deg*phi(i),mu(1,i-2),mu(2,i-2),
+ & -b2(1,i-2),b2(2,i-2),b1(1,i-2),b1(2,i-2),
+ & dsqrt(b2(1,i-1)**2+b2(2,i-1)**2)
+ & +dsqrt(b1(1,i-1)**2+b1(2,i-1)**2),
+ & ((ee(l,k,i-2),l=1,2),k=1,2),eenew(1,itype2loc(iti))
+#endif
cd write (iout,*) 'mu1',mu1(:,i-2)
cd write (iout,*) 'mu2',mu2(:,i-2)
if (wcorr4.gt.0.0d0 .or. wcorr5.gt.0.0d0 .or.wcorr6.gt.0.0d0)
#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
C
C 14/01/2014 TURN3,TUNR4 does no go under periodic boundry condition
do i=iturn3_start,iturn3_end
+c if (i.le.1) cycle
+C write(iout,*) "tu jest i",i
if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1
+C changes suggested by Ana to avoid out of bounds
+C Adam: Unnecessary: handled by iturn3_end and iturn3_start
+c & .or.((i+4).gt.nres)
+c & .or.((i-1).le.0)
+C end of changes by Ana
& .or. itype(i+2).eq.ntyp1
- & .or. itype(i+3).eq.ntyp1
- & .or. itype(i-1).eq.ntyp1
- & .or. itype(i+4).eq.ntyp1
- & ) cycle
+ & .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)
num_cont_hb(i)=num_conti
enddo
do i=iturn4_start,iturn4_end
+ if (i.lt.1) cycle
if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1
+C changes suggested by Ana to avoid out of bounds
+c & .or.((i+5).gt.nres)
+c & .or.((i-1).le.0)
+C end of changes suggested by Ana
& .or. itype(i+3).eq.ntyp1
& .or. itype(i+4).eq.ntyp1
- & .or. itype(i+5).eq.ntyp1
- & .or. itype(i).eq.ntyp1
- & .or. itype(i-1).eq.ntyp1
+c & .or. itype(i+5).eq.ntyp1
+c & .or. itype(i).eq.ntyp1
+c & .or. itype(i-1).eq.ntyp1
& ) cycle
dxi=dc(1,i)
dyi=dc(2,i)
c
c Loop over all pairs of interacting peptide groups except i,i+2 and i,i+3
c
+CTU KURWA
do i=iatel_s,iatel_e
+C do i=75,75
+c if (i.le.1) cycle
if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1
- & .or. itype(i+2).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)
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)
+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
- & .or.itype(j+2).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
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),
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
el1=fac3*(4.0D0+fac*fac-3.0D0*(cosb*cosb+cosg*cosg))
el2=fac4*fac
C MARYSIA
- eesij=(el1+el2)
+C eesij=(el1+el2)
C 12/26/95 - for the evaluation of multi-body H-bonding interactions
ees0ij=4.0D0+fac*fac-3.0D0*(cosb*cosb+cosg*cosg)
+ if (shield_mode.gt.0) then
+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
+ 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,
write (iout,'(a6,2i5,0pf7.3,2i5,2e11.3)')
&'evdw1',i,j,evdwij
&,iteli,itelj,aaa,evdw1
- write (iout,'(a6,2i5,0pf7.3)') 'ees',i,j,eesij
+ write (iout,*) sss
+ write (iout,'(a6,2i5,0pf7.3,2f8.3)') 'ees',i,j,eesij,
+ &fac_shield(i),fac_shield(j)
endif
C
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.
*
* 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
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
C Contribution to the local-electrostatic energy coming from the i-j pair
eel_loc_ij=a22*muij(1)+a23*muij(2)+a32*muij(3)
& +a33*muij(4)
+ if (shield_mode.eq.0) then
+ fac_shield(i)=1.0
+ fac_shield(j)=1.0
+C else
+C fac_shield(i)=0.4
+C fac_shield(j)=0.6
+ endif
+ eel_loc_ij=eel_loc_ij
+ & *fac_shield(i)*fac_shield(j)
+C Now derivative over eel_loc
+ if ((fac_shield(i).gt.0).and.(fac_shield(j).gt.0).and.
+ & (shield_mode.gt.0)) then
+C print *,i,j
+
+ do ilist=1,ishield_list(i)
+ iresshield=shield_list(ilist,i)
+ do k=1,3
+ rlocshield=grad_shield_side(k,ilist,i)*eel_loc_ij
+ & /fac_shield(i)
+C & *2.0
+ gshieldx_ll(k,iresshield)=gshieldx_ll(k,iresshield)+
+ & rlocshield
+ & +grad_shield_loc(k,ilist,i)*eel_loc_ij/fac_shield(i)
+ gshieldc_ll(k,iresshield-1)=gshieldc_ll(k,iresshield-1)
+ & +rlocshield
+ enddo
+ enddo
+ do ilist=1,ishield_list(j)
+ iresshield=shield_list(ilist,j)
+ do k=1,3
+ rlocshield=grad_shield_side(k,ilist,j)*eel_loc_ij
+ & /fac_shield(j)
+C & *2.0
+ gshieldx_ll(k,iresshield)=gshieldx_ll(k,iresshield)+
+ & rlocshield
+ & +grad_shield_loc(k,ilist,j)*eel_loc_ij/fac_shield(j)
+ gshieldc_ll(k,iresshield-1)=gshieldc_ll(k,iresshield-1)
+ & +rlocshield
+
+ enddo
+ enddo
+
+ do k=1,3
+ gshieldc_ll(k,i)=gshieldc_ll(k,i)+
+ & grad_shield(k,i)*eel_loc_ij/fac_shield(i)
+ gshieldc_ll(k,j)=gshieldc_ll(k,j)+
+ & grad_shield(k,j)*eel_loc_ij/fac_shield(j)
+ gshieldc_ll(k,i-1)=gshieldc_ll(k,i-1)+
+ & grad_shield(k,i)*eel_loc_ij/fac_shield(i)
+ gshieldc_ll(k,j-1)=gshieldc_ll(k,j-1)+
+ & grad_shield(k,j)*eel_loc_ij/fac_shield(j)
+ enddo
+ endif
+
+
c write (iout,*) 'i',i,' j',j,itype(i),itype(j),
c & ' eel_loc_ij',eel_loc_ij
-c write(iout,*) 'muije=',muij(1),muij(2),muij(3),muij(4)
+C write(iout,*) 'muije=',i,j,muij(1),muij(2),muij(3),muij(4)
C Calculate patrial derivative for theta angle
#ifdef NEWCORR
- geel_loc_ij=a22*gmuij1(1)
+ geel_loc_ij=(a22*gmuij1(1)
& +a23*gmuij1(2)
& +a32*gmuij1(3)
- & +a33*gmuij1(4)
+ & +a33*gmuij1(4))
+ & *fac_shield(i)*fac_shield(j)
c write(iout,*) "derivative over thatai"
c write(iout,*) a22*gmuij1(1), a23*gmuij1(2) ,a32*gmuij1(3),
c & a33*gmuij1(4)
& +a33*gmuij2(4)
gloc(nphi+i-1,icg)=gloc(nphi+i-1,icg)+
& geel_loc_ij*wel_loc
+ & *fac_shield(i)*fac_shield(j)
+
c Derivative over j residue
geel_loc_ji=a22*gmuji1(1)
& +a23*gmuji1(2)
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)
c & a33*gmuji2(4)
gloc(nphi+j-1,icg)=gloc(nphi+j-1,icg)+
& geel_loc_ji*wel_loc
+ & *fac_shield(i)*fac_shield(j)
#endif
cd write (iout,*) 'i',i,' j',j,' eel_loc_ij',eel_loc_ij
C Partial derivatives in virtual-bond dihedral angles gamma
if (i.gt.1)
& gel_loc_loc(i-1)=gel_loc_loc(i-1)+
- & a22*muder(1,i)*mu(1,j)+a23*muder(1,i)*mu(2,j)
- & +a32*muder(2,i)*mu(1,j)+a33*muder(2,i)*mu(2,j)
+ & (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)
do l=1,3
gel_loc(l,i)=gel_loc(l,i)+(aggi(l,1)*muij(1)+
& aggi(l,2)*muij(2)+aggi(l,3)*muij(3)+aggi(l,4)*muij(4))
+ & *fac_shield(i)*fac_shield(j)
+
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),
call matmat2(a_temp(1,1),auxmat1(1,1),pizda(1,1))
call matmat2(a_temp(1,1),auxgmatt1(1,1),gpizda1(1,1))
call matmat2(a_temp(1,1),auxgmatt2(1,1),gpizda2(1,1))
+ if (shield_mode.eq.0) then
+ fac_shield(i)=1.0
+ fac_shield(j)=1.0
+C else
+C fac_shield(i)=0.4
+C fac_shield(j)=0.6
+ endif
eello_turn3=eello_turn3+0.5d0*(pizda(1,1)+pizda(2,2))
+ & *fac_shield(i)*fac_shield(j)
+ eello_t3=0.5d0*(pizda(1,1)+pizda(2,2))
+ & *fac_shield(i)*fac_shield(j)
+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
- if (energy_dec) write (iout,'(a6,2i5,0pf7.3)')
- & 'eturn3',i,j,0.5d0*(pizda(1,1)+pizda(2,2))
+C if (energy_dec) write (iout,'(a6,2i5,0pf7.3)')
+C Derivatives in shield mode
+ if ((fac_shield(i).gt.0).and.(fac_shield(j).gt.0).and.
+ & (shield_mode.gt.0)) then
+C print *,i,j
+
+ do ilist=1,ishield_list(i)
+ iresshield=shield_list(ilist,i)
+ do k=1,3
+ rlocshield=grad_shield_side(k,ilist,i)*eello_t3/fac_shield(i)
+C & *2.0
+ gshieldx_t3(k,iresshield)=gshieldx_t3(k,iresshield)+
+ & rlocshield
+ & +grad_shield_loc(k,ilist,i)*eello_t3/fac_shield(i)
+ gshieldc_t3(k,iresshield-1)=gshieldc_t3(k,iresshield-1)
+ & +rlocshield
+ enddo
+ enddo
+ do ilist=1,ishield_list(j)
+ iresshield=shield_list(ilist,j)
+ do k=1,3
+ rlocshield=grad_shield_side(k,ilist,j)*eello_t3/fac_shield(j)
+C & *2.0
+ gshieldx_t3(k,iresshield)=gshieldx_t3(k,iresshield)+
+ & rlocshield
+ & +grad_shield_loc(k,ilist,j)*eello_t3/fac_shield(j)
+ gshieldc_t3(k,iresshield-1)=gshieldc_t3(k,iresshield-1)
+ & +rlocshield
+
+ enddo
+ enddo
+
+ do k=1,3
+ gshieldc_t3(k,i)=gshieldc_t3(k,i)+
+ & grad_shield(k,i)*eello_t3/fac_shield(i)
+ gshieldc_t3(k,j)=gshieldc_t3(k,j)+
+ & grad_shield(k,j)*eello_t3/fac_shield(j)
+ gshieldc_t3(k,i-1)=gshieldc_t3(k,i-1)+
+ & grad_shield(k,i)*eello_t3/fac_shield(i)
+ gshieldc_t3(k,j-1)=gshieldc_t3(k,j-1)+
+ & grad_shield(k,j)*eello_t3/fac_shield(j)
+ enddo
+ endif
+
+C if (energy_dec) write (iout,'(a6,2i5,0pf7.3)')
cd write (2,*) 'i,',i,' j',j,'eello_turn3',
cd & 0.5d0*(pizda(1,1)+pizda(2,2)),
cd & ' eello_turn3_num',4*eello_turn3_num
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),
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))
gsEE1=0.5d0*(gtEpizda1(1,1)+gtEpizda1(2,2))
gsEE2=0.5d0*(gtEpizda2(1,1)+gtEpizda2(2,2))
gsEE3=0.5d0*(gtEpizda3(1,1)+gtEpizda3(2,2))
-
+ if (shield_mode.eq.0) then
+ fac_shield(i)=1.0
+ fac_shield(j)=1.0
+C else
+C fac_shield(i)=0.6
+C fac_shield(j)=0.4
+ endif
eello_turn4=eello_turn4-(s1+s2+s3)
+ & *fac_shield(i)*fac_shield(j)
+ eello_t4=-(s1+s2+s3)
+ & *fac_shield(i)*fac_shield(j)
c write(iout,*)'chujOWO', auxvec(1),b1(1,iti2)
if (energy_dec) write (iout,'(a6,2i5,0pf7.3,3f7.3)')
& 'eturn4',i,j,-(s1+s2+s3),s1,s2,s3
+C Now derivative over shield:
+ if ((fac_shield(i).gt.0).and.(fac_shield(j).gt.0).and.
+ & (shield_mode.gt.0)) then
+C print *,i,j
+
+ do ilist=1,ishield_list(i)
+ iresshield=shield_list(ilist,i)
+ do k=1,3
+ rlocshield=grad_shield_side(k,ilist,i)*eello_t4/fac_shield(i)
+C & *2.0
+ gshieldx_t4(k,iresshield)=gshieldx_t4(k,iresshield)+
+ & rlocshield
+ & +grad_shield_loc(k,ilist,i)*eello_t4/fac_shield(i)
+ gshieldc_t4(k,iresshield-1)=gshieldc_t4(k,iresshield-1)
+ & +rlocshield
+ enddo
+ enddo
+ do ilist=1,ishield_list(j)
+ iresshield=shield_list(ilist,j)
+ do k=1,3
+ rlocshield=grad_shield_side(k,ilist,j)*eello_t4/fac_shield(j)
+C & *2.0
+ gshieldx_t4(k,iresshield)=gshieldx_t4(k,iresshield)+
+ & rlocshield
+ & +grad_shield_loc(k,ilist,j)*eello_t4/fac_shield(j)
+ gshieldc_t4(k,iresshield-1)=gshieldc_t4(k,iresshield-1)
+ & +rlocshield
+
+ enddo
+ enddo
+
+ do k=1,3
+ gshieldc_t4(k,i)=gshieldc_t4(k,i)+
+ & grad_shield(k,i)*eello_t4/fac_shield(i)
+ gshieldc_t4(k,j)=gshieldc_t4(k,j)+
+ & grad_shield(k,j)*eello_t4/fac_shield(j)
+ gshieldc_t4(k,i-1)=gshieldc_t4(k,i-1)+
+ & grad_shield(k,i)*eello_t4/fac_shield(i)
+ gshieldc_t4(k,j-1)=gshieldc_t4(k,j-1)+
+ & grad_shield(k,j)*eello_t4/fac_shield(j)
+ enddo
+ endif
+
+
+
+
+
+
cd write (2,*) 'i,',i,' j',j,'eello_turn4',-(s1+s2+s3),
cd & ' eello_turn4_num',8*eello_turn4_num
#ifdef NEWCORR
gloc(nphi+i,icg)=gloc(nphi+i,icg)
& -(gs13+gsE13+gsEE1)*wturn4
+ & *fac_shield(i)*fac_shield(j)
gloc(nphi+i+1,icg)= gloc(nphi+i+1,icg)
& -(gs23+gs21+gsEE2)*wturn4
+ & *fac_shield(i)*fac_shield(j)
+
gloc(nphi+i+2,icg)= gloc(nphi+i+2,icg)
& -(gs32+gsE31+gsEE3)*wturn4
+ & *fac_shield(i)*fac_shield(j)
+
c gloc(nphi+i+1,icg)=gloc(nphi+i+1,icg)-
c & gs2
#endif
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))
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))
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
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
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)
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)
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)
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.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
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. iabs(itype(iii)).eq.1 .and.
- & iabs(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. itype(iii).eq.1 .and. itype(jjj).eq.1) then
+ if (ii.gt.nres .and. iabs(itype(iii)).eq.1 .and.
+ & iabs(itype(jjj)).eq.1) then
call ssbond_ene(iii,jjj,eij)
ehpb=ehpb+2*eij
endif
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,'(a6,2i5,3f8.3)') "edisl",ii,jj,
+ & ehpb,fordepth(i),dd
+ else
+ if (dhpb1(i).gt.0.0d0) then
+ ehpb=ehpb+2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
+ fac=forcon(i)*gnmr1prim(dd,dhpb(i),dhpb1(i))/dd
+c write (iout,*) "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)
+ 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,'(a6,2i5,3f8.3)') "edisl",ii,jj,
+ & ehpb,fordepth(i),dd
+ else
+ if (dhpb1(i).gt.0.0d0) then
+ ehpb=ehpb+2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
+ fac=forcon(i)*gnmr1prim(dd,dhpb(i),dhpb1(i))/dd
+c write (iout,*) "alph nmr",
+c & dd,2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
+ else
rdis=dd-dhpb(i)
C Get the force constant corresponding to this distance.
waga=forcon(i)
C Calculate the contribution to energy.
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
+ endif
+ endif
do j=1,3
ggg(j)=fac*(c(j,jj)-c(j,ii))
enddo
enddo
endif
enddo
- ehpb=0.5D0*ehpb
+ if (constr_dist.ne.11) ehpb=0.5D0*ehpb
return
end
C--------------------------------------------------------------------------
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
c write (iout,'(i5,3f10.5)') i,(gradb(j,i-1),j=1,3)
c endif
enddo
+
estr=0.5d0*AKP*estr+estr1
c
c 09/18/07 AL: multimodal bond potential based on AM1 CA-SC PMF's included
end
#ifdef CRYST_THETA
C--------------------------------------------------------------------------
- subroutine ebend(etheta)
+ subroutine ebend(etheta,ethetacnstr)
C
C Evaluate the virtual-bond-angle energy given the virtual-bond dihedral
C angles gamma and its derivatives in consecutive thetas and gammas.
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
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)
enddo
+ 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=ethetcnstr+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=ethetcnstr+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
+
C Ufff.... We've done all this!!!
return
end
end
#else
C--------------------------------------------------------------------------
- subroutine ebend(etheta)
+ subroutine ebend(etheta,ethetacnstr)
C
C Evaluate the virtual-bond-angle energy given the virtual-bond dihedral
C angles gamma and its derivatives in consecutive thetas and gammas.
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),
c print *,i,itype(i-1),itype(i),itype(i-2)
if ((itype(i-1).eq.ntyp1).or.itype(i-2).eq.ntyp1
& .or.itype(i).eq.ntyp1) cycle
-C In current verion the ALL DUMMY ATOM POTENTIALS ARE OFF
-
+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
coskt(k)=dcos(k*theti2)
sinkt(k)=dsin(k*theti2)
enddo
+C print *,ethetai
if (i.gt.3 .and. itype(i-3).ne.ntyp1) then
#ifdef OSF
phii=phi(i)
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
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
write(iout,*) "ethetai",ethetai
endif
+C print *,ethetai
do m=1,ntheterm2
do k=1,nsingle
aux=bbthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph1(k)
& 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
enddo
10 continue
c lprn1=.true.
+C print *,ethetai
if (lprn1)
& write (iout,'(i2,3f8.1,9h ethetai ,f10.5)')
& i,theta(i)*rad2deg,phii*rad2deg,
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)=gloc(nphi+i-2,icg)+wang*dethetai
+ enddo
+C now constrains
+ 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
#endif
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
+ 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*difi**4
- gloc(itori-3,icg)=gloc(itori-3,icg)+ftors*difi**3
+ edihcnstr=edihcnstr+0.25d0*ftors(i)**difi**4
+ gloc(itori-3,icg)=gloc(itori-3,icg)+ftors(i)*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)
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
+ 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*difi**4
- gloc(itori-3,icg)=gloc(itori-3,icg)+ftors*difi**3
+ 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
-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)
+ if (energy_dec) then
+ write (iout,'(a6,2i5,4f8.3,2e14.5)') "edihc",
+ & i,itori,rad2deg*phii,
+ & rad2deg*phi0(i), rad2deg*drange(i),
+ & rad2deg*difi,0.25d0*ftors(i)*difi**4,gloc(itori-3,icg)
+ endif
enddo
cd write (iout,*) 'edihcnstr',edihcnstr
return
return
end
#endif
-c------------------------------------------------------------------------------
- subroutine eback_sc_corr(esccor)
-c 7/21/2007 Correlations between the backbone-local and side-chain-local
-c conformational states; temporarily implemented as differences
-c between UNRES torsional potentials (dependent on three types of
+C----------------------------------------------------------------------------------
+C The rigorous attempt to derive energy function
+ subroutine etor_kcc(etors,edihcnstr)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.VAR'
+ include 'COMMON.GEO'
+ include 'COMMON.LOCAL'
+ include 'COMMON.TORSION'
+ include 'COMMON.INTERACT'
+ include 'COMMON.DERIV'
+ include 'COMMON.CHAIN'
+ include 'COMMON.NAMES'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.FFIELD'
+ include 'COMMON.TORCNSTR'
+ include 'COMMON.CONTROL'
+ logical lprn
+c double precision thybt1(maxtermkcc),thybt2(maxtermkcc)
+C Set lprn=.true. for debugging
+ lprn=.false.
+c lprn=.true.
+C print *,"wchodze kcc"
+ if (lprn) write (iout,*) "etor_kcc tor_mode",tor_mode
+ if (tor_mode.ne.2) then
+ etors=0.0D0
+ endif
+ do i=iphi_start,iphi_end
+C ANY TWO ARE DUMMY ATOMS in row CYCLE
+c if (((itype(i-3).eq.ntyp1).and.(itype(i-2).eq.ntyp1)).or.
+c & ((itype(i-2).eq.ntyp1).and.(itype(i-1).eq.ntyp1)) .or.
+c & ((itype(i-1).eq.ntyp1).and.(itype(i).eq.ntyp1))) cycle
+ if (itype(i-2).eq.ntyp1.or. itype(i-1).eq.ntyp1
+ & .or. itype(i).eq.ntyp1 .or. itype(i-3).eq.ntyp1) cycle
+ itori=itortyp_kcc(itype(i-2))
+ itori1=itortyp_kcc(itype(i-1))
+ phii=phi(i)
+ glocig=0.0D0
+ glocit1=0.0d0
+ glocit2=0.0d0
+ sumnonchebyshev=0.0d0
+ sumchebyshev=0.0d0
+C to avoid multiple devision by 2
+c theti22=0.5d0*theta(i)
+C theta 12 is the theta_1 /2
+C theta 22 is theta_2 /2
+c theti12=0.5d0*theta(i-1)
+C and appropriate sinus function
+ sinthet1=dsin(theta(i-1))
+ sinthet2=dsin(theta(i))
+ costhet1=dcos(theta(i-1))
+ costhet2=dcos(theta(i))
+c Cosines of halves thetas
+ costheti12=0.5d0*(1.0d0+costhet1)
+ costheti22=0.5d0*(1.0d0+costhet2)
+C to speed up lets store its mutliplication
+ sint1t2=sinthet2*sinthet1
+ sint1t2n=1.0d0
+C \sum_{i=1}^n (sin(theta_1) * sin(theta_2))^n * (c_n* cos(n*gamma)
+C +d_n*sin(n*gamma)) *
+C \sum_{i=1}^m (1+a_m*Tb_m(cos(theta_1 /2))+b_m*Tb_m(cos(theta_2 /2)))
+C we have two sum 1) Non-Chebyshev which is with n and gamma
+ etori=0.0d0
+ do j=1,nterm_kcc(itori,itori1)
+
+ nval=nterm_kcc_Tb(itori,itori1)
+ v1ij=v1_kcc(j,itori,itori1)
+ v2ij=v2_kcc(j,itori,itori1)
+c write (iout,*) "i",i," j",j," v1",v1ij," v2",v2ij
+C v1ij is c_n and d_n in euation above
+ cosphi=dcos(j*phii)
+ sinphi=dsin(j*phii)
+ sint1t2n1=sint1t2n
+ sint1t2n=sint1t2n*sint1t2
+ sumth1tyb1=tschebyshev(1,nval,v11_chyb(1,j,itori,itori1),
+ & costheti12)
+ gradth1tyb1=-0.5d0*sinthet1*gradtschebyshev(0,nval-1,
+ & v11_chyb(1,j,itori,itori1),costheti12)
+c write (iout,*) "v11",(v11_chyb(k,j,itori,itori1),k=1,nval),
+c & " sumth1tyb1",sumth1tyb1," gradth1tyb1",gradth1tyb1
+ sumth2tyb1=tschebyshev(1,nval,v21_chyb(1,j,itori,itori1),
+ & costheti22)
+ gradth2tyb1=-0.5d0*sinthet2*gradtschebyshev(0,nval-1,
+ & v21_chyb(1,j,itori,itori1),costheti22)
+c write (iout,*) "v21",(v21_chyb(k,j,itori,itori1),k=1,nval),
+c & " sumth2tyb1",sumth2tyb1," gradth2tyb1",gradth2tyb1
+ sumth1tyb2=tschebyshev(1,nval,v12_chyb(1,j,itori,itori1),
+ & costheti12)
+ gradth1tyb2=-0.5d0*sinthet1*gradtschebyshev(0,nval-1,
+ & v12_chyb(1,j,itori,itori1),costheti12)
+c write (iout,*) "v12",(v12_chyb(k,j,itori,itori1),k=1,nval),
+c & " sumth1tyb2",sumth1tyb2," gradth1tyb2",gradth1tyb2
+ sumth2tyb2=tschebyshev(1,nval,v22_chyb(1,j,itori,itori1),
+ & costheti22)
+ gradth2tyb2=-0.5d0*sinthet2*gradtschebyshev(0,nval-1,
+ & v22_chyb(1,j,itori,itori1),costheti22)
+c write (iout,*) "v22",(v22_chyb(k,j,itori,itori1),k=1,nval),
+c & " sumth2tyb2",sumth2tyb2," gradth2tyb2",gradth2tyb2
+C etors=etors+sint1t2n*(v1ij*cosphi+v2ij*sinphi)
+C if (energy_dec) etors_ii=etors_ii+
+C & v1ij*cosphi+v2ij*sinphi
+C glocig is the gradient local i site in gamma
+ actval1=v1ij*cosphi*(1.0d0+sumth1tyb1+sumth2tyb1)
+ actval2=v2ij*sinphi*(1.0d0+sumth1tyb2+sumth2tyb2)
+ etori=etori+sint1t2n*(actval1+actval2)
+ glocig=glocig+
+ & j*sint1t2n*(v2ij*cosphi*(1.0d0+sumth1tyb2+sumth2tyb2)
+ & -v1ij*sinphi*(1.0d0+sumth1tyb1+sumth2tyb1))
+C now gradient over theta_1
+ glocit1=glocit1+
+ & j*sint1t2n1*costhet1*sinthet2*(actval1+actval2)+
+ & sint1t2n*(v1ij*cosphi*gradth1tyb1+v2ij*sinphi*gradth1tyb2)
+ glocit2=glocit2+
+ & j*sint1t2n1*sinthet1*costhet2*(actval1+actval2)+
+ & sint1t2n*(v1ij*cosphi*gradth2tyb1+v2ij*sinphi*gradth2tyb2)
+
+C now the Czebyshev polinominal sum
+c do k=1,nterm_kcc_Tb(itori,itori1)
+c thybt1(k)=v1_chyb(k,j,itori,itori1)
+c thybt2(k)=v2_chyb(k,j,itori,itori1)
+C thybt1(k)=0.0
+C thybt2(k)=0.0
+c enddo
+C print *, sumth1thyb, gradthybt1, sumth2thyb, gradthybt2,
+C & gradtschebyshev
+C & (0,nterm_kcc_Tb(itori,itori1)-1,thybt2(1),
+C & dcos(theti22)**2),
+C & dsin(theti22)
+
+C now overal sumation
+C print *,"sumnon", sumnonchebyshev,sumth1thyb+sumth2thyb
+ enddo ! j
+ etors=etors+etori
+C derivative over gamma
+ gloc(i-3,icg)=gloc(i-3,icg)+wtor*glocig
+C derivative over theta1
+ gloc(nphi+i-3,icg)=gloc(nphi+i-3,icg)+wtor*glocit1
+C now derivative over theta2
+ gloc(nphi+i-2,icg)=gloc(nphi+i-2,icg)+wtor*glocit2
+ if (lprn)
+ & write (iout,*) i-2,i-1,itype(i-2),itype(i-1),itori,itori1,
+ & theta(i-1)*rad2deg,theta(i)*rad2deg,phii*rad2deg,etori
+ enddo
+C gloc(i-3,icg)=gloc(i-3,icg)+wtor*gloci
+! 6/20/98 - dihedral angle constraints
+ if (tor_mode.ne.2) then
+ edihcnstr=0.0d0
+c do i=1,ndih_constr
+ do i=idihconstr_start,idihconstr_end
+ itori=idih_constr(i)
+ phii=phi(itori)
+ difi=pinorm(phii-phi0(i))
+ if (difi.gt.drange(i)) then
+ difi=difi-drange(i)
+ edihcnstr=edihcnstr+0.25d0*ftors(i)*difi**4
+ gloc(itori-3,icg)=gloc(itori-3,icg)+ftors(i)*difi**3
+ else if (difi.lt.-drange(i)) then
+ difi=difi+drange(i)
+ edihcnstr=edihcnstr+0.25d0*ftors(i)*difi**4
+ gloc(itori-3,icg)=gloc(itori-3,icg)+ftors(i)*difi**3
+ else
+ difi=0.0
+ endif
+ enddo
+ endif
+ return
+ end
+
+C The rigorous attempt to derive energy function
+ subroutine ebend_kcc(etheta,ethetacnstr)
+
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.VAR'
+ include 'COMMON.GEO'
+ include 'COMMON.LOCAL'
+ include 'COMMON.TORSION'
+ include 'COMMON.INTERACT'
+ include 'COMMON.DERIV'
+ include 'COMMON.CHAIN'
+ include 'COMMON.NAMES'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.FFIELD'
+ include 'COMMON.TORCNSTR'
+ include 'COMMON.CONTROL'
+ logical lprn
+ double precision thybt1(maxtermkcc)
+C Set lprn=.true. for debugging
+ lprn=.false.
+c lprn=.true.
+C print *,"wchodze kcc"
+ if (lprn) write (iout,*) "ebend_kcc tor_mode",tor_mode
+ if (tor_mode.ne.2) etheta=0.0D0
+ do i=ithet_start,ithet_end
+c print *,i,itype(i-1),itype(i),itype(i-2)
+ if ((itype(i-1).eq.ntyp1).or.itype(i-2).eq.ntyp1
+ & .or.itype(i).eq.ntyp1) cycle
+ iti=itortyp_kcc(itype(i-1))
+ sinthet=dsin(theta(i)/2.0d0)
+ costhet=dcos(theta(i)/2.0d0)
+ do j=1,nbend_kcc_Tb(iti)
+ thybt1(j)=v1bend_chyb(j,iti)
+ enddo
+ sumth1thyb=tschebyshev
+ & (1,nbend_kcc_Tb(iti),thybt1(1),costhet)
+ if (lprn) write (iout,*) i-1,itype(i-1),iti,theta(i)*rad2deg,
+ & sumth1thyb
+ ihelp=nbend_kcc_Tb(iti)-1
+ gradthybt1=gradtschebyshev
+ & (0,ihelp,thybt1(1),costhet)
+ etheta=etheta+sumth1thyb
+C print *,sumth1thyb,gradthybt1,sinthet*(-0.5d0)
+ gloc(nphi+i-2,icg)=gloc(nphi+i-2,icg)+wang*
+ & gradthybt1*sinthet*(-0.5d0)
+ enddo
+ if (tor_mode.ne.2) then
+ ethetacnstr=0.0d0
+C print *,ithetaconstr_start,ithetaconstr_end,"TU"
+ do i=ithetaconstr_start,ithetaconstr_end
+ itheta=itheta_constr(i)
+ thetiii=theta(itheta)
+ difi=pinorm(thetiii-theta_constr0(i))
+ if (difi.gt.theta_drange(i)) then
+ difi=difi-theta_drange(i)
+ ethetacnstr=ethetacnstr+0.25d0*for_thet_constr(i)*difi**4
+ gloc(itheta+nphi-2,icg)=gloc(itheta+nphi-2,icg)
+ & +for_thet_constr(i)*difi**3
+ else if (difi.lt.-drange(i)) then
+ difi=difi+drange(i)
+ ethetacnstr=ethetacnstr+0.25d0*for_thet_constr(i)*difi**4
+ gloc(itheta+nphi-2,icg)=gloc(itheta+nphi-2,icg)
+ & +for_thet_constr(i)*difi**3
+ else
+ difi=0.0
+ endif
+ if (energy_dec) then
+ write (iout,'(a6,2i5,4f8.3,2e14.5)') "ethetc",
+ & i,itheta,rad2deg*thetiii,
+ & rad2deg*theta_constr0(i), rad2deg*theta_drange(i),
+ & rad2deg*difi,0.25d0*for_thet_constr(i)*difi**4,
+ & gloc(itheta+nphi-2,icg)
+ endif
+ enddo
+ endif
+ return
+ end
+c------------------------------------------------------------------------------
+ subroutine eback_sc_corr(esccor)
+c 7/21/2007 Correlations between the backbone-local and side-chain-local
+c conformational states; temporarily implemented as differences
+c between UNRES torsional potentials (dependent on three types of
c residues) and the torsional potentials dependent on all 20 types
c of residues computed from AM1 energy surfaces of terminally-blocked
c amino-acid residues.
include 'COMMON.DERIV'
include 'COMMON.INTERACT'
include 'COMMON.CONTACTS'
+ include 'COMMON.SHIELD'
double precision gx(3),gx1(3)
logical lprn
lprn=.false.
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
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
+ itj1=nloctyp
endif
do iii=1,2
dipi(iii,1)=Ub2(iii,i)
if (l.eq.j+1) then
C parallel orientation of the two CA-CA-CA frames.
if (i.gt.1) then
- iti=itortyp(itype(i))
+ iti=itype2loc(itype(i))
else
- iti=ntortyp
+ iti=nloctyp
endif
- itk1=itortyp(itype(k+1))
- itj=itortyp(itype(j))
+ itk1=itype2loc(itype(k+1))
+ itj=itype2loc(itype(j))
if (l.lt.nres-1) then
- itl1=itortyp(itype(l+1))
+ itl1=itype2loc(itype(l+1))
else
- itl1=ntortyp
+ itl1=nloctyp
endif
C A1 kernel(j+1) A2T
cd do iii=1,2
else
C Antiparallel orientation of the two CA-CA-CA frames.
if (i.gt.1) then
- iti=itortyp(itype(i))
+ iti=itype2loc(itype(i))
else
- iti=ntortyp
+ iti=nloctyp
endif
- itk1=itortyp(itype(k+1))
- itl=itortyp(itype(l))
- itj=itortyp(itype(j))
+ itk1=itype2loc(itype(k+1))
+ itl=itype2loc(itype(l))
+ itj=itype2loc(itype(j))
if (j.lt.nres-1) then
- itj1=itortyp(itype(j+1))
+ itj1=itype2loc(itype(j+1))
else
- itj1=ntortyp
+ itj1=nloctyp
endif
C A2 kernel(j-1)T A1T
call kernel(aa1(1,1),aa2t(1,1),a_chuj_der(1,1,1,1,jj,i),
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)
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)
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)
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))
C energy moment and not to the cluster cumulant.
iti=itortyp(itype(i))
if (j.lt.nres-1) then
- itj1=itortyp(itype(j+1))
+ itj1=itype2loc(itype(j+1))
else
- itj1=ntortyp
+ itj1=nloctyp
endif
- itk=itortyp(itype(k))
- itk1=itortyp(itype(k+1))
+ itk=itype2loc(itype(k))
+ itk1=itype2loc(itype(k+1))
if (l.lt.nres-1) then
- itl1=itortyp(itype(l+1))
+ itl1=itype2loc(itype(l+1))
else
- itl1=ntortyp
+ itl1=nloctyp
endif
#ifdef MOMENT
s1=dip(4,jj,i)*dip(4,kk,k)
s2=0.5d0*scalar2(b1(1,k),auxvec(1))
call matvec2(AECA(1,1,2),b1(1,l+1),auxvec(1))
s3=0.5d0*scalar2(b1(1,j+1),auxvec(1))
- call transpose2(EE(1,1,itk),auxmat(1,1))
+ call transpose2(EE(1,1,k),auxmat(1,1))
call matmat2(auxmat(1,1),AECA(1,1,1),pizda(1,1))
vv(1)=pizda(1,1)+pizda(2,2)
vv(2)=pizda(2,1)-pizda(1,2)
C 4/7/01 AL Component s1 was removed, because it pertains to the respective
C energy moment and not to the cluster cumulant.
cd write (2,*) 'eello_graph4: wturn6',wturn6
- iti=itortyp(itype(i))
- itj=itortyp(itype(j))
+ iti=itype2loc(itype(i))
+ itj=itype2loc(itype(j))
if (j.lt.nres-1) then
- itj1=itortyp(itype(j+1))
+ itj1=itype2loc(itype(j+1))
else
- itj1=ntortyp
+ itj1=nloctyp
endif
- itk=itortyp(itype(k))
+ itk=itype2loc(itype(k))
if (k.lt.nres-1) then
- itk1=itortyp(itype(k+1))
+ itk1=itype2loc(itype(k+1))
else
- itk1=ntortyp
+ itk1=nloctyp
endif
- itl=itortyp(itype(l))
+ itl=itype2loc(itype(l))
if (l.lt.nres-1) then
- itl1=itortyp(itype(l+1))
+ itl1=itype2loc(itype(l+1))
else
- itl1=ntortyp
+ itl1=nloctyp
endif
cd write (2,*) 'eello6_graph4:','i',i,' j',j,' k',k,' l',l
cd write (2,*) 'iti',iti,' itj',itj,' itj1',itj1,' itk',itk,
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
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
+ VofOverlap=VSolvSphere/2.0d0*(1.0d0-dsqrt(1.0d0-sinphi*sinthet))
+ & /VSolvSphere_div
+C & *wshield
+C now the gradient...
+ do j=1,3
+ grad_shield(j,i)=grad_shield(j,i)
+C gradient po skalowaniu
+ & +(sh_frac_dist_grad(j)*VofOverlap
+C gradient po costhet
+ & +scale_fac_dist*VSolvSphere/VSolvSphere_div/4.0d0*
+ &(1.0d0/(-dsqrt(1.0d0-sinphi*sinthet))*(
+ & sinphi/sinthet*costhet*costhet_grad(j)
+ & +sinthet/sinphi*cosphi*cosphi_grad_long(j)))
+ & )*wshield
+C grad_shield_side is Cbeta sidechain gradient
+ grad_shield_side(j,ishield_list(i),i)=
+ & (sh_frac_dist_grad(j)*-2.0d0
+ & *VofOverlap
+ & -scale_fac_dist*VSolvSphere/VSolvSphere_div/2.0d0*
+ &(1.0d0/(-dsqrt(1.0d0-sinphi*sinthet))*(
+ & sinphi/sinthet*costhet*costhet_grad(j)
+ & +sinthet/sinphi*cosphi*cosphi_grad_long(j)))
+ & )*wshield
+
+ grad_shield_loc(j,ishield_list(i),i)=
+ & scale_fac_dist*VSolvSphere/VSolvSphere_div/2.0d0*
+ &(1.0d0/(dsqrt(1.0d0-sinphi*sinthet))*(
+ & sinthet/sinphi*cosphi*cosphi_grad_loc(j)
+ & ))
+ & *wshield
+ enddo
+ VolumeTotal=VolumeTotal+VofOverlap*scale_fac_dist
+ enddo
+ fac_shield(i)=VolumeTotal*wshield+(1.0d0-wshield)
+C write(2,*) "TOTAL VOLUME",i,VolumeTotal,fac_shield(i)
+ 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)=(c(1,i)+c(1,i+1))/2.0d0-tubecenter(1)
+ vectube(2)=(c(2,i)+c(2,i+1))/2.0d0-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)-tubecenter(1)
+ vectube(2)=c(2,i+nres)-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
projects / unres.git / blobdiff