C
C Calculate the virtual-bond-angle energy.
C
- call ebend(ebe)
C print *,'Bend energy finished.'
+ call ebend(ebe,ethetacnstr)
+cd print *,'Bend energy finished.'
C
C Calculate the SC local energy.
C
C 21/5/07 Calculate local sicdechain correlation energy
C
call eback_sc_corr(esccor)
+
+ if (wliptran.gt.0) then
+ call Eliptransfer(eliptran)
+ endif
+
C
C 12/1/95 Multi-body terms
C
etot=wsc*(evdw+fact(6)*evdw_t)+wscp*evdw2+welec*fact(1)*ees
& +wvdwpp*evdw1
& +wang*ebe+wtor*fact(1)*etors+wscloc*escloc
- & +wstrain*ehpb+nss*ebr+wcorr*fact(3)*ecorr+wcorr5*fact(4)*ecorr5
+ & +wstrain*ehpb+wcorr*fact(3)*ecorr+wcorr5*fact(4)*ecorr5
& +wcorr6*fact(5)*ecorr6+wturn4*fact(3)*eello_turn4
& +wturn3*fact(2)*eello_turn3+wturn6*fact(5)*eturn6
& +wel_loc*fact(2)*eel_loc+edihcnstr+wtor_d*fact(2)*etors_d
- & +wbond*estr+wsccor*fact(1)*esccor
+ & +wbond*estr+wsccor*fact(1)*esccor+ethetacnstr
+ & +wliptran*eliptran
#else
etot=wsc*(evdw+fact(6)*evdw_t)+wscp*evdw2
& +welec*fact(1)*(ees+evdw1)
& +wang*ebe+wtor*fact(1)*etors+wscloc*escloc
- & +wstrain*ehpb+nss*ebr+wcorr*fact(3)*ecorr+wcorr5*fact(4)*ecorr5
+ & +wstrain*ehpb+wcorr*fact(3)*ecorr+wcorr5*fact(4)*ecorr5
& +wcorr6*fact(5)*ecorr6+wturn4*fact(3)*eello_turn4
& +wturn3*fact(2)*eello_turn3+wturn6*fact(5)*eturn6
& +wel_loc*fact(2)*eel_loc+edihcnstr+wtor_d*fact(2)*etors_d
- & +wbond*estr+wsccor*fact(1)*esccor
+ & +wbond*estr+wsccor*fact(1)*esccor+ethetacnstr
+ & +wliptran*eliptran
#endif
energia(0)=etot
energia(1)=evdw
energia(19)=esccor
energia(20)=edihcnstr
energia(21)=evdw_t
+ energia(24)=ethetacnstr
+ energia(22)=eliptran
c detecting NaNQ
#ifdef ISNAN
#ifdef AIX
& wcorr6*fact(5)*gradcorr6(j,i)+
& wturn6*fact(5)*gcorr6_turn(j,i)+
& wsccor*fact(2)*gsccorc(j,i)
+ & +wliptran*gliptranc(j,i)
gradx(j,i,icg)=wsc*gvdwx(j,i)+wscp*gradx_scp(j,i)+
& wbond*gradbx(j,i)+
& wstrain*ghpbx(j,i)+wcorr*gradxorr(j,i)+
& wsccor*fact(2)*gsccorx(j,i)
+ & +wliptran*gliptranx(j,i)
enddo
#else
do i=1,nct
& wcorr6*fact(5)*gradcorr6(j,i)+
& wturn6*fact(5)*gcorr6_turn(j,i)+
& wsccor*fact(2)*gsccorc(j,i)
+ & +wliptran*gliptranc(j,i)
gradx(j,i,icg)=wsc*gvdwx(j,i)+wscp*gradx_scp(j,i)+
& wbond*gradbx(j,i)+
& wstrain*ghpbx(j,i)+wcorr*gradxorr(j,i)+
& wsccor*fact(1)*gsccorx(j,i)
+ & +wliptran*gliptranx(j,i)
enddo
#endif
enddo
& +wturn3*fact(2)*gel_loc_turn3(i)
& +wturn6*fact(5)*gel_loc_turn6(i)
& +wel_loc*fact(2)*gel_loc_loc(i)
+c & +wsccor*fact(1)*gsccor_loc(i)
+c BYLA ROZNICA Z CLUSTER< OSTATNIA LINIA DODANA
enddo
endif
+ if (dyn_ss) call dyn_set_nss
return
end
C------------------------------------------------------------------------
esccor=energia(19)
edihcnstr=energia(20)
estr=energia(18)
+ ethetacnstr=energia(24)
+ eliptran=energia(22)
#ifdef SPLITELE
write (iout,10) evdw,wsc,evdw2,wscp,ees,welec*fact(1),evdw1,
& wvdwpp,
& ecorr,wcorr*fact(3),ecorr5,wcorr5*fact(4),ecorr6,wcorr6*fact(5),
& eel_loc,wel_loc*fact(2),eello_turn3,wturn3*fact(2),
& eello_turn4,wturn4*fact(3),eello_turn6,wturn6*fact(5),
- & esccor,wsccor*fact(1),edihcnstr,ebr*nss,etot
+ & esccor,wsccor*fact(1),edihcnstr,ethetacnstr,ebr*nss,
+ & eliptran,wliptran,etot
10 format (/'Virtual-chain energies:'//
& 'EVDW= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-SC)'/
& 'EVDW2= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-p)'/
& 'ETURN6=',1pE16.6,' WEIGHT=',1pD16.6,' (turns, 6th order)'/
& 'ESCCOR=',1pE16.6,' WEIGHT=',1pD16.6,' (backbone-rotamer corr)'/
& 'EDIHC= ',1pE16.6,' (dihedral angle constraints)'/
+ & 'ETHETC= ',1pE16.6,' (valence angle constraints)'/
& 'ESS= ',1pE16.6,' (disulfide-bridge intrinsic energy)'/
+ & 'ELT=',1pE16.6, ' WEIGHT=',1pD16.6,' (Lipid transfer energy)'/
& 'ETOT= ',1pE16.6,' (total)')
#else
write (iout,10) evdw,wsc,evdw2,wscp,ees,welec*fact(1),estr,wbond,
& ecorr6,wcorr6*fact(5),eel_loc,wel_loc*fact(2),
& eello_turn3,wturn3*fact(2),eello_turn4,wturn4*fact(3),
& eello_turn6,wturn6*fact(5),esccor*fact(1),wsccor,
- & edihcnstr,ebr*nss,etot
+ & edihcnstr,ethetacnstr,ebr*nss,eliptran,wliptran,etot
10 format (/'Virtual-chain energies:'//
& 'EVDW= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-SC)'/
& 'EVDW2= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-p)'/
& 'ETURN6=',1pE16.6,' WEIGHT=',1pD16.6,' (turns, 6th order)'/
& 'ESCCOR=',1pE16.6,' WEIGHT=',1pD16.6,' (backbone-rotamer corr)'/
& 'EDIHC= ',1pE16.6,' (dihedral angle constraints)'/
+ & 'ETHETC= ',1pE16.6,' (valence angle constraints)'/
& 'ESS= ',1pE16.6,' (disulfide-bridge intrinsic energy)'/
+ & 'ELT=',1pE16.6, ' WEIGHT=',1pD16.6,' (Lipid transfer energy)'/
& 'ETOT= ',1pE16.6,' (total)')
#endif
return
integer icant
external icant
cd print *,'Entering ELJ nnt=',nnt,' nct=',nct,' expon=',expon
+c ROZNICA z cluster
do i=1,210
do j=1,2
eneps_temp(j,i)=0.0d0
enddo
enddo
+cROZNICA
+
evdw=0.0D0
evdw_t=0.0d0
do i=iatsc_s,iatsc_e
c write (iout,*)'i=',i,' j=',j,' itypi=',itypi,' itypj=',itypj
eps0ij=eps(itypi,itypj)
fac=rrij**expon2
- e1=fac*fac*aa(itypi,itypj)
- e2=fac*bb(itypi,itypj)
+ e1=fac*fac*aa
+ e2=fac*bb
evdwij=e1+e2
ij=icant(itypi,itypj)
+c ROZNICA z cluster
eneps_temp(1,ij)=eneps_temp(1,ij)+e1/dabs(eps0ij)
eneps_temp(2,ij)=eneps_temp(2,ij)+e2/eps0ij
+c
+
cd sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
cd epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
cd write (iout,'(2(a3,i3,2x),6(1pd12.4)/2(3(1pd12.4),5x)/)')
cd & restyp(itypi),i,restyp(itypj),j,aa(itypi,itypj),
cd & bb(itypi,itypj),1.0D0/dsqrt(rrij),evdwij,epsi,sigm,
cd & (c(k,i),k=1,3),(c(k,j),k=1,3)
- if (bb(itypi,itypj).gt.0.0d0) then
+ if (bb.gt.0.0d0) then
evdw=evdw+evdwij
else
evdw_t=evdw_t+evdwij
rij=1.0D0/r_inv_ij
r_shift_inv=1.0D0/(rij+r0(itypi,itypj)-sigma(itypi,itypj))
fac=r_shift_inv**expon
- e1=fac*fac*aa(itypi,itypj)
- e2=fac*bb(itypi,itypj)
+ e1=fac*fac*aa
+ e2=fac*bb
evdwij=e_augm+e1+e2
ij=icant(itypi,itypj)
eneps_temp(1,ij)=eneps_temp(1,ij)+(e1+a_augm)
cd & bb(itypi,itypj),augm(itypi,itypj),epsi,sigm,
cd & sigma(itypi,itypj),1.0D0/dsqrt(rrij),evdwij,
cd & (c(k,i),k=1,3),(c(k,j),k=1,3)
- if (bb(itypi,itypj).gt.0.0d0) then
+ if (bb.gt.0.0d0) then
evdw=evdw+evdwij
else
evdw_t=evdw_t+evdwij
C Calculate whole angle-dependent part of epsilon and contributions
C to its derivatives
fac=(rrij*sigsq)**expon2
- e1=fac*fac*aa(itypi,itypj)
- e2=fac*bb(itypi,itypj)
+ e1=fac*fac*aa
+ e2=fac*bb
evdwij=eps1*eps2rt*eps3rt*(e1+e2)
eps2der=evdwij*eps3rt
eps3der=evdwij*eps2rt
eneps_temp(1,ij)=eneps_temp(1,ij)+e1*aux
& /dabs(eps(itypi,itypj))
eneps_temp(2,ij)=eneps_temp(2,ij)+e2*aux/eps(itypi,itypj)
- if (bb(itypi,itypj).gt.0.0d0) then
+ if (bb.gt.0.0d0) then
evdw=evdw+evdwij
else
evdw_t=evdw_t+evdwij
endif
if (calc_grad) then
if (lprn) then
- sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
- epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
+ sigm=dabs(aa/bb)**(1.0D0/6.0D0)
+ epsi=bb**2/aa
write (iout,'(2(a3,i3,2x),15(0pf7.3))')
& restyp(itypi),i,restyp(itypj),j,
& epsi,sigm,chi1,chi2,chip1,chip2,
include 'COMMON.ENEPS'
include 'COMMON.IOUNITS'
include 'COMMON.CALC'
+ include 'COMMON.SBRIDGE'
logical lprn
common /srutu/icall
integer icant
if (yi.lt.0) yi=yi+boxysize
zi=mod(zi,boxzsize)
if (zi.lt.0) zi=zi+boxzsize
+ if ((zi.gt.bordlipbot)
+ &.and.(zi.lt.bordliptop)) then
+C the energy transfer exist
+ if (zi.lt.buflipbot) then
+C what fraction I am in
+ fracinbuf=1.0d0-
+ & ((zi-bordlipbot)/lipbufthick)
+C lipbufthick is thickenes of lipid buffore
+ sslipi=sscalelip(fracinbuf)
+ ssgradlipi=-sscagradlip(fracinbuf)/lipbufthick
+ elseif (zi.gt.bufliptop) then
+ fracinbuf=1.0d0-((bordliptop-zi)/lipbufthick)
+ sslipi=sscalelip(fracinbuf)
+ ssgradlipi=sscagradlip(fracinbuf)/lipbufthick
+ else
+ sslipi=1.0d0
+ ssgradlipi=0.0
+ endif
+ else
+ sslipi=0.0d0
+ ssgradlipi=0.0
+ endif
dxi=dc_norm(1,nres+i)
dyi=dc_norm(2,nres+i)
C
do iint=1,nint_gr(i)
do j=istart(i,iint),iend(i,iint)
+ IF (dyn_ss_mask(i).and.dyn_ss_mask(j)) THEN
+ call dyn_ssbond_ene(i,j,evdwij)
+ evdw=evdw+evdwij
+C write (iout,'(a6,2i5,0pf7.3,a3,2f10.3)')
+C & 'evdw',i,j,evdwij,' ss',evdw,evdw_t
+C triple bond artifac removal
+ do k=j+1,iend(i,iint)
+C search over all next residues
+ if (dyn_ss_mask(k)) then
+C check if they are cysteins
+C write(iout,*) 'k=',k
+ call triple_ssbond_ene(i,j,k,evdwij)
+C call the energy function that removes the artifical triple disulfide
+C bond the soubroutine is located in ssMD.F
+ evdw=evdw+evdwij
+C write (iout,'(a6,2i5,0pf7.3,a3,2f10.3)')
+C & 'evdw',i,j,evdwij,'tss',evdw,evdw_t
+ endif!dyn_ss_mask(k)
+ enddo! k
+ ELSE
ind=ind+1
itypj=iabs(itype(j))
if (itypj.eq.ntyp1) cycle
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,*),aa,aa_lip(itypi,itypj),aa_aq(itypi,itypj)
C checking the distance
dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
xj_safe=xj
if (sss.le.0.0) cycle
C Calculate angle-dependent terms of energy and contributions to their
C derivatives.
+
call sc_angular
sigsq=1.0D0/sigsq
sig=sig0ij*dsqrt(sigsq)
c---------------------------------------------------------------
rij_shift=1.0D0/rij_shift
fac=rij_shift**expon
- e1=fac*fac*aa(itypi,itypj)
- e2=fac*bb(itypi,itypj)
+ e1=fac*fac*aa
+ e2=fac*bb
evdwij=eps1*eps2rt*eps3rt*(e1+e2)
eps2der=evdwij*eps3rt
eps3der=evdwij*eps2rt
evdwij=evdwij*eps2rt*eps3rt
- if (bb(itypi,itypj).gt.0) then
+ if (bb.gt.0) then
evdw=evdw+evdwij*sss
else
evdw_t=evdw_t+evdwij*sss
c & " ij",ij," eneps",aux*e1/dabs(eps(itypi,itypj)),
c & aux*e2/eps(itypi,itypj)
c if (lprn) then
- sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
- epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
+ sigm=dabs(aa/bb)**(1.0D0/6.0D0)
+ epsi=bb**2/aa
#ifdef DEBUG
write (iout,'(2(a3,i3,2x),17(0pf7.3))')
& restyp(itypi),i,restyp(itypj),j,
C Calculate angular part of the gradient.
call sc_grad
endif
+C write(iout,*) "partial sum", evdw, evdw_t
+ ENDIF ! dyn_ss
enddo ! j
enddo ! iint
enddo ! i
c---------------------------------------------------------------
rij_shift=1.0D0/rij_shift
fac=rij_shift**expon
- e1=fac*fac*aa(itypi,itypj)
- e2=fac*bb(itypi,itypj)
+ e1=fac*fac*aa
+ e2=fac*bb
evdwij=eps1*eps2rt*eps3rt*(e1+e2)
eps2der=evdwij*eps3rt
eps3der=evdwij*eps2rt
fac_augm=rrij**expon
e_augm=augm(itypi,itypj)*fac_augm
evdwij=evdwij*eps2rt*eps3rt
- if (bb(itypi,itypj).gt.0.0d0) then
+ if (bb.gt.0.0d0) then
evdw=evdw+evdwij+e_augm
else
evdw_t=evdw_t+evdwij+e_augm
do k=1,2
mu(k,i-2)=Ub2(k,i-2)+b1(k,iti1)
enddo
+C write (iout,*) 'mumu',i,b1(1,iti),Ub2(1,i-2)
+
C Vectors and matrices dependent on a single virtual-bond dihedral.
call matvec2(DD(1,1,iti),b1tilde(1,iti1),auxvec(1))
call matvec2(Ug2(1,1,i-2),auxvec(1),Ug2Db1t(1,i-2))
eel_loc_ij=a22*muij(1)+a23*muij(2)+a32*muij(3)
& +a33*muij(4)
c write (iout,*) 'i',i,' j',j,' eel_loc_ij',eel_loc_ij
-c write (iout,'(a6,2i5,0pf7.3)')
-c & 'eelloc',i,j,eel_loc_ij
+C write (iout,'(a6,2i5,0pf7.3)')
+C & 'eelloc',i,j,eel_loc_ij
+C write(iout,*) 'muije=',i,j,muij(1),muij(2),muij(3),muij(4)
c write (iout,*) a22,muij(1),a23,muij(2),a32,muij(3)
eel_loc=eel_loc+eel_loc_ij
C Partial derivatives in virtual-bond dihedral angles gamma
enddo
endif
else if (j.eq.i+3 .and. itype(i+2).ne.ntyp1) then
+ if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1
+C changes suggested by Ana to avoid out of bounds
+ & .or.((i+5).gt.nres)
+ & .or.((i-1).le.0)
+C 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) goto 178
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
C
C Fourth-order contributions
gcorr4_turn(l,j1)=gcorr4_turn(l,j1)-(s1+s2+s3)
enddo
endif
+ 178 continue
endif
return
end
include 'COMMON.DERIV'
include 'COMMON.VAR'
include 'COMMON.INTERACT'
+ include 'COMMON.CONTROL'
+ include 'COMMON.IOUNITS'
dimension ggg(3)
ehpb=0.0D0
cd print *,'edis: nhpb=',nhpb,' fbr=',fbr
cd print *,'link_start=',link_start,' link_end=',link_end
+C write(iout,*) link_end, "link_end"
if (link_end.eq.0) return
do i=link_start,link_end
C If ihpb(i) and jhpb(i) > NRES, this is a SC-SC distance, otherwise a
endif
C 24/11/03 AL: SS bridges handled separately because of introducing a specific
C distance and angle dependent SS bond potential.
- if (ii.gt.nres .and. iabs(itype(iii)).eq.1 .and.
+C if (ii.gt.nres .and. iabs(itype(iii)).eq.1 .and.
+C & iabs(itype(jjj)).eq.1) then
+C write(iout,*) constr_dist,"const"
+ if (.not.dyn_ss .and. i.le.nss) then
+ if (ii.gt.nres .and. iabs(itype(iii)).eq.1 .and.
& iabs(itype(jjj)).eq.1) then
call ssbond_ene(iii,jjj,eij)
ehpb=ehpb+2*eij
- else
-C Calculate the distance between the two points and its difference from the
-C target distance.
- dd=dist(ii,jj)
- rdis=dd-dhpb(i)
+ endif !ii.gt.neres
+ else if (ii.gt.nres .and. jj.gt.nres) then
+c Restraints from contact prediction
+ dd=dist(ii,jj)
+ if (constr_dist.eq.11) then
+C ehpb=ehpb+fordepth(i)**4.0d0
+C & *rlornmr1(dd,dhpb(i),dhpb1(i),forcon(i))
+ ehpb=ehpb+fordepth(i)**4.0d0
+ & *rlornmr1(dd,dhpb(i),dhpb1(i),forcon(i))
+ fac=fordepth(i)**4.0d0
+ & *rlornmr1prim(dd,dhpb(i),dhpb1(i),forcon(i))/dd
+C write (iout,'(a6,2i5,3f8.3)') "edisl",ii,jj,
+C & ehpb,fordepth(i),dd
+C write(iout,*) ehpb,"atu?"
+C ehpb,"tu?"
+C fac=fordepth(i)**4.0d0
+C & *rlornmr1prim(dd,dhpb(i),dhpb1(i),forcon(i))/dd
+ else
+ if (dhpb1(i).gt.0.0d0) then
+ ehpb=ehpb+2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
+ fac=forcon(i)*gnmr1prim(dd,dhpb(i),dhpb1(i))/dd
+c write (iout,*) "beta nmr",
+c & dd,2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
+ else
+ dd=dist(ii,jj)
+ rdis=dd-dhpb(i)
+C Get the force constant corresponding to this distance.
+ waga=forcon(i)
+C Calculate the contribution to energy.
+ ehpb=ehpb+waga*rdis*rdis
+c write (iout,*) "beta reg",dd,waga*rdis*rdis
+C
+C Evaluate gradient.
+C
+ fac=waga*rdis/dd
+ endif !end dhpb1(i).gt.0
+ endif !end const_dist=11
+ do j=1,3
+ ggg(j)=fac*(c(j,jj)-c(j,ii))
+ enddo
+ do j=1,3
+ ghpbx(j,iii)=ghpbx(j,iii)-ggg(j)
+ ghpbx(j,jjj)=ghpbx(j,jjj)+ggg(j)
+ enddo
+ do k=1,3
+ ghpbc(k,jjj)=ghpbc(k,jjj)+ggg(k)
+ ghpbc(k,iii)=ghpbc(k,iii)-ggg(k)
+ enddo
+ else !ii.gt.nres
+C write(iout,*) "before"
+ dd=dist(ii,jj)
+C write(iout,*) "after",dd
+ if (constr_dist.eq.11) then
+ ehpb=ehpb+fordepth(i)**4.0d0
+ & *rlornmr1(dd,dhpb(i),dhpb1(i),forcon(i))
+ fac=fordepth(i)**4.0d0
+ & *rlornmr1prim(dd,dhpb(i),dhpb1(i),forcon(i))/dd
+C ehpb=ehpb+fordepth(i)**4*rlornmr1(dd,dhpb(i),dhpb1(i))
+C fac=fordepth(i)**4*rlornmr1prim(dd,dhpb(i),dhpb1(i))/dd
+C print *,ehpb,"tu?"
+C write(iout,*) ehpb,"btu?",
+C & dd,dhpb(i),dhpb1(i),fordepth(i),forcon(i)
+C write (iout,'(a6,2i5,3f8.3)') "edisl",ii,jj,
+C & ehpb,fordepth(i),dd
+ else
+ if (dhpb1(i).gt.0.0d0) then
+ ehpb=ehpb+2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
+ fac=forcon(i)*gnmr1prim(dd,dhpb(i),dhpb1(i))/dd
+c write (iout,*) "alph nmr",
+c & dd,2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
+ else
+ rdis=dd-dhpb(i)
C Get the force constant corresponding to this distance.
- waga=forcon(i)
+ waga=forcon(i)
C Calculate the contribution to energy.
- ehpb=ehpb+waga*rdis*rdis
+ ehpb=ehpb+waga*rdis*rdis
+c write (iout,*) "alpha reg",dd,waga*rdis*rdis
C
C Evaluate gradient.
C
- fac=waga*rdis/dd
-cd print *,'i=',i,' ii=',ii,' jj=',jj,' dhpb=',dhpb(i),' dd=',dd,
-cd & ' waga=',waga,' fac=',fac
+ fac=waga*rdis/dd
+ endif
+ endif
+
do j=1,3
ggg(j)=fac*(c(j,jj)-c(j,ii))
enddo
enddo
endif
enddo
- ehpb=0.5D0*ehpb
+ if (constr_dist.ne.11) ehpb=0.5D0*ehpb
return
end
C--------------------------------------------------------------------------
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.IOUNITS'
include 'COMMON.NAMES'
include 'COMMON.FFIELD'
+ include 'COMMON.TORCNSTR'
common /calcthet/ term1,term2,termm,diffak,ratak,
& ak,aktc,termpre,termexp,sigc,sig0i,time11,time12,sigcsq,
& delthe0,sig0inv,sigtc,sigsqtc,delthec,it
double precision y(2),z(2)
delta=0.02d0*pi
- time11=dexp(-2*time)
- time12=1.0d0
+c time11=dexp(-2*time)
+c time12=1.0d0
etheta=0.0D0
c write (iout,*) "nres",nres
c write (*,'(a,i2)') 'EBEND ICG=',icg
if (i.gt.3 .and. itype(i-3).ne.ntyp1) then
#ifdef OSF
phii=phi(i)
- icrc=0
- call proc_proc(phii,icrc)
+c icrc=0
+c call proc_proc(phii,icrc)
if (icrc.eq.1) phii=150.0
#else
phii=phi(i)
if (i.lt.nres .and. itype(i+1).ne.ntyp1) then
#ifdef OSF
phii1=phi(i+1)
- icrc=0
- call proc_proc(phii1,icrc)
+c icrc=0
+c call proc_proc(phii1,icrc)
if (icrc.eq.1) phii1=150.0
phii1=pinorm(phii1)
z(1)=cos(phii1)
if (i.gt.3) gloc(i-3,icg)=gloc(i-3,icg)+wang*E_tc*dthetg1
if (i.lt.nres) gloc(i-2,icg)=gloc(i-2,icg)+wang*E_tc*dthetg2
gloc(nphi+i-2,icg)=wang*(E_theta+E_tc*dthett)
- 1215 continue
+c 1215 continue
+ enddo
+ ethetacnstr=0.0d0
+C print *,ithetaconstr_start,ithetaconstr_end,"TU"
+ do i=1,ntheta_constr
+ itheta=itheta_constr(i)
+ thetiii=theta(itheta)
+ difi=pinorm(thetiii-theta_constr0(i))
+ if (difi.gt.theta_drange(i)) then
+ difi=difi-theta_drange(i)
+ ethetacnstr=ethetacnstr+0.25d0*for_thet_constr(i)*difi**4
+ gloc(itheta+nphi-2,icg)=gloc(itheta+nphi-2,icg)
+ & +for_thet_constr(i)*difi**3
+ else if (difi.lt.-drange(i)) then
+ difi=difi+drange(i)
+ ethetacnstr=ethetacnstr+0.25d0*for_thet_constr(i)*difi**4
+ gloc(itheta+nphi-2,icg)=gloc(itheta+nphi-2,icg)
+ & +for_thet_constr(i)*difi**3
+ else
+ difi=0.0
+ endif
+C if (energy_dec) then
+C write (iout,'(a6,2i5,4f8.3,2e14.5)') "ethetc",
+C & i,itheta,rad2deg*thetiii,
+C & rad2deg*theta_constr0(i), rad2deg*theta_drange(i),
+C & rad2deg*difi,0.25d0*for_thet_constr(i)*difi**4,
+C & gloc(itheta+nphi-2,icg)
+ endif
enddo
C Ufff.... We've done all this!!!
return
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),
enddo
else
phii=0.0d0
- ityp1=nthetyp+1
+c ityp1=nthetyp+1
do k=1,nsingle
+ ityp1=ithetyp((itype(i-2)))
cosph1(k)=0.0d0
sinph1(k)=0.0d0
enddo
enddo
else
phii1=0.0d0
- ityp3=nthetyp+1
+c ityp3=nthetyp+1
+ ityp3=ithetyp((itype(i)))
do k=1,nsingle
cosph2(k)=0.0d0
sinph2(k)=0.0d0
etheta=etheta+ethetai
if (i.gt.3) gloc(i-3,icg)=gloc(i-3,icg)+wang*dephii
if (i.lt.nres) gloc(i-2,icg)=gloc(i-2,icg)+wang*dephii1
- gloc(nphi+i-2,icg)=wang*dethetai
+c gloc(nphi+i-2,icg)=wang*dethetai
+ gloc(nphi+i-2,icg)=gloc(nphi+i-2,icg)+wang*dethetai
+ enddo
+C now constrains
+ ethetacnstr=0.0d0
+C print *,ithetaconstr_start,ithetaconstr_end,"TU"
+ do i=1,ntheta_constr
+ itheta=itheta_constr(i)
+ thetiii=theta(itheta)
+ difi=pinorm(thetiii-theta_constr0(i))
+ if (difi.gt.theta_drange(i)) then
+ difi=difi-theta_drange(i)
+ ethetacnstr=ethetacnstr+0.25d0*for_thet_constr(i)*difi**4
+ gloc(itheta+nphi-2,icg)=gloc(itheta+nphi-2,icg)
+ & +for_thet_constr(i)*difi**3
+ else if (difi.lt.-drange(i)) then
+ difi=difi+drange(i)
+ ethetacnstr=ethetacnstr+0.25d0*for_thet_constr(i)*difi**4
+ gloc(itheta+nphi-2,icg)=gloc(itheta+nphi-2,icg)
+ & +for_thet_constr(i)*difi**3
+ else
+ difi=0.0
+ endif
+C if (energy_dec) then
+C write (iout,'(a6,2i5,4f8.3,2e14.5)') "ethetc",
+C & i,itheta,rad2deg*thetiii,
+C & rad2deg*theta_constr0(i), rad2deg*theta_drange(i),
+C & rad2deg*difi,0.25d0*for_thet_constr(i)*difi**4,
+C & gloc(itheta+nphi-2,icg)
+C endif
enddo
return
end
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)
+C write (iout,'(a6,2i5,2f8.3,2e14.5)') "edih",
+C & i,itori,rad2deg*phii,
+C & rad2deg*difi,0.25d0*ftors(i)*difi**4,gloc(itori-3,icg)
enddo
! write (iout,*) 'edihcnstr',edihcnstr
return
edihi=0.0d0
if (difi.gt.drange(i)) then
difi=difi-drange(i)
- edihcnstr=edihcnstr+0.25d0*ftors*difi**4
- gloc(itori-3,icg)=gloc(itori-3,icg)+ftors*difi**3
- edihi=0.25d0*ftors*difi**4
+ edihcnstr=edihcnstr+0.25d0*ftors(i)*difi**4
+ gloc(itori-3,icg)=gloc(itori-3,icg)+ftors(i)*difi**3
+ edihi=0.25d0*ftors(i)*difi**4
else if (difi.lt.-drange(i)) then
difi=difi+drange(i)
- edihcnstr=edihcnstr+0.25d0*ftors*difi**4
- gloc(itori-3,icg)=gloc(itori-3,icg)+ftors*difi**3
- edihi=0.25d0*ftors*difi**4
+ edihcnstr=edihcnstr+0.25d0*ftors(i)*difi**4
+ gloc(itori-3,icg)=gloc(itori-3,icg)+ftors(i)*difi**3
+ edihi=0.25d0*ftors(i)*difi**4
else
difi=0.0d0
endif
+ write (iout,'(a6,2i5,2f8.3,2e14.5)') "edih",
+ & i,itori,rad2deg*phii,
+ & rad2deg*difi,0.25d0*ftors(i)*difi**4
c write (iout,'(2i5,4f10.5,e15.5)') i,itori,phii,phi0(i),difi,
c & drange(i),edihi
! write (iout,'(2i5,2f8.3,2e14.5)') i,itori,rad2deg*phii,
-! & rad2deg*difi,0.25d0*ftors*difi**4,gloc(itori-3,icg)
+! & rad2deg*difi,0.25d0*ftors(i)*difi**4,gloc(itori-3,icg)
enddo
! write (iout,*) 'edihcnstr',edihcnstr
return
esccor=esccor+v1ij*cosphi+v2ij*sinphi
gloci=gloci+j*(v2ij*cosphi-v1ij*sinphi)
enddo
+C write (iout,*)"EBACK_SC_COR",esccor,i
c write (iout,*) "EBACK_SC_COR",i,v1ij*cosphi+v2ij*sinphi,intertyp,
c & nterm_sccor(isccori,isccori1),isccori,isccori1
c gloc_sc(intertyp,i-3,icg)=gloc_sc(intertyp,i-3,icg)+wsccor*gloci
return
end
crc-------------------------------------------------
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+ subroutine Eliptransfer(eliptran)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.LOCAL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CALC'
+ include 'COMMON.CONTROL'
+ include 'COMMON.SPLITELE'
+ include 'COMMON.SBRIDGE'
+C this is done by Adasko
+C print *,"wchodze"
+C structure of box:
+C water
+C--bordliptop-- buffore starts
+C--bufliptop--- here true lipid starts
+C lipid
+C--buflipbot--- lipid ends buffore starts
+C--bordlipbot--buffore ends
+ eliptran=0.0
+ do i=1,nres
+C do i=1,1
+ if (itype(i).eq.ntyp1) cycle
+
+ positi=(mod(((c(3,i)+c(3,i+1))/2.0d0),boxzsize))
+ if (positi.le.0) positi=positi+boxzsize
+C print *,i
+C first for peptide groups
+c for each residue check if it is in lipid or lipid water border area
+ if ((positi.gt.bordlipbot)
+ &.and.(positi.lt.bordliptop)) then
+C the energy transfer exist
+ if (positi.lt.buflipbot) then
+C what fraction I am in
+ fracinbuf=1.0d0-
+ & ((positi-bordlipbot)/lipbufthick)
+C lipbufthick is thickenes of lipid buffore
+ sslip=sscalelip(fracinbuf)
+ ssgradlip=-sscagradlip(fracinbuf)/lipbufthick
+ eliptran=eliptran+sslip*pepliptran
+ gliptranc(3,i)=gliptranc(3,i)+ssgradlip*pepliptran/2.0d0
+ gliptranc(3,i-1)=gliptranc(3,i-1)+ssgradlip*pepliptran/2.0d0
+C gliptranc(3,i-2)=gliptranc(3,i)+ssgradlip*pepliptran
+ elseif (positi.gt.bufliptop) then
+ fracinbuf=1.0d0-((bordliptop-positi)/lipbufthick)
+ sslip=sscalelip(fracinbuf)
+ ssgradlip=sscagradlip(fracinbuf)/lipbufthick
+ eliptran=eliptran+sslip*pepliptran
+ gliptranc(3,i)=gliptranc(3,i)+ssgradlip*pepliptran/2.0d0
+ gliptranc(3,i-1)=gliptranc(3,i-1)+ssgradlip*pepliptran/2.0d0
+C gliptranc(3,i-2)=gliptranc(3,i)+ssgradlip*pepliptran
+C print *, "doing sscalefor top part"
+C print *,i,sslip,fracinbuf,ssgradlip
+ else
+ eliptran=eliptran+pepliptran
+C print *,"I am in true lipid"
+ endif
+C else
+C eliptran=elpitran+0.0 ! I am in water
+ endif
+ enddo
+C print *, "nic nie bylo w lipidzie?"
+C now multiply all by the peptide group transfer factor
+C eliptran=eliptran*pepliptran
+C now the same for side chains
+CV do i=1,1
+ do i=1,nres
+ if (itype(i).eq.ntyp1) cycle
+ positi=(mod(c(3,i+nres),boxzsize))
+ if (positi.le.0) positi=positi+boxzsize
+C print *,mod(c(3,i+nres),boxzsize),bordlipbot,bordliptop
+c for each residue check if it is in lipid or lipid water border area
+C respos=mod(c(3,i+nres),boxzsize)
+C print *,positi,bordlipbot,buflipbot
+ if ((positi.gt.bordlipbot)
+ & .and.(positi.lt.bordliptop)) then
+C the energy transfer exist
+ if (positi.lt.buflipbot) then
+ fracinbuf=1.0d0-
+ & ((positi-bordlipbot)/lipbufthick)
+C lipbufthick is thickenes of lipid buffore
+ sslip=sscalelip(fracinbuf)
+ ssgradlip=-sscagradlip(fracinbuf)/lipbufthick
+ eliptran=eliptran+sslip*liptranene(itype(i))
+ gliptranx(3,i)=gliptranx(3,i)
+ &+ssgradlip*liptranene(itype(i))
+ gliptranc(3,i-1)= gliptranc(3,i-1)
+ &+ssgradlip*liptranene(itype(i))
+C print *,"doing sccale for lower part"
+ elseif (positi.gt.bufliptop) then
+ fracinbuf=1.0d0-
+ &((bordliptop-positi)/lipbufthick)
+ sslip=sscalelip(fracinbuf)
+ ssgradlip=sscagradlip(fracinbuf)/lipbufthick
+ eliptran=eliptran+sslip*liptranene(itype(i))
+ gliptranx(3,i)=gliptranx(3,i)
+ &+ssgradlip*liptranene(itype(i))
+ gliptranc(3,i-1)= gliptranc(3,i-1)
+ &+ssgradlip*liptranene(itype(i))
+C print *, "doing sscalefor top part",sslip,fracinbuf
+ else
+ eliptran=eliptran+liptranene(itype(i))
+C print *,"I am in true lipid"
+ endif
+ endif ! if in lipid or buffor
+C else
+C eliptran=elpitran+0.0 ! I am in water
+ enddo
+ return
+ end
+
+
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+
SUBROUTINE MATVEC2(A1,V1,V2)
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
return
end
C-----------------------------------------------------------------------
+C-----------------------------------------------------------------------
+ double precision function sscalelip(r)
+ double precision r,gamm
+ include "COMMON.SPLITELE"
+C if(r.lt.r_cut-rlamb) then
+C sscale=1.0d0
+C else if(r.le.r_cut.and.r.ge.r_cut-rlamb) then
+C gamm=(r-(r_cut-rlamb))/rlamb
+ sscalelip=1.0d0+r*r*(2*r-3.0d0)
+C else
+C sscale=0d0
+C endif
+ return
+ end
+C-----------------------------------------------------------------------
+ double precision function sscagradlip(r)
+ double precision r,gamm
+ include "COMMON.SPLITELE"
+C if(r.lt.r_cut-rlamb) then
+C sscagrad=0.0d0
+C else if(r.le.r_cut.and.r.ge.r_cut-rlamb) then
+C gamm=(r-(r_cut-rlamb))/rlamb
+ sscagradlip=r*(6*r-6.0d0)
+C else
+C sscagrad=0.0d0
+C endif
+ return
+ end
+
+C-----------------------------------------------------------------------
projects / unres.git / blobdiff