include 'COMMON.TIME1'
include 'COMMON.SPLITELE'
include 'COMMON.SHIELD'
+ double precision fac_shieldbuf(maxres),
+ & grad_shield_locbuf(3,maxcontsshi,-1:maxres),
+ & grad_shield_sidebuf(3,maxcontsshi,-1:maxres),
+ & grad_shieldbuf(3,-1:maxres)
+ integer ishield_listbuf(maxres),
+ &shield_listbuf(maxcontsshi,maxres)
#ifdef MPI
c print*,"ETOTAL Processor",fg_rank," absolute rank",myrank,
c & " nfgtasks",nfgtasks
& grad_shield_side(1,1,i),grad_shield_loc(1,1,i)
enddo
#endif
- call MPI_Allgatherv(fac_shield(ivec_start),ivec_count(fg_rank1),
- & MPI_DOUBLE_PRECISION,fac_shield(1),ivec_count(0),ivec_displ(0),
+ call MPI_Allgatherv(fac_shield(ivec_start),
+ & ivec_count(fg_rank1),
+ & MPI_DOUBLE_PRECISION,fac_shieldbuf(1),ivec_count(0),
+ & ivec_displ(0),
& MPI_DOUBLE_PRECISION,FG_COMM,IERR)
call MPI_Allgatherv(shield_list(1,ivec_start),
& ivec_count(fg_rank1),
- & MPI_I50,shield_list(1,1),ivec_count(0),
+ & MPI_I50,shield_listbuf(1,1),ivec_count(0),
& ivec_displ(0),
& MPI_I50,FG_COMM,IERR)
call MPI_Allgatherv(ishield_list(ivec_start),
& ivec_count(fg_rank1),
- & MPI_INTEGER,ishield_list(1),ivec_count(0),
+ & MPI_INTEGER,ishield_listbuf(1),ivec_count(0),
& ivec_displ(0),
& MPI_INTEGER,FG_COMM,IERR)
call MPI_Allgatherv(grad_shield(1,ivec_start),
& ivec_count(fg_rank1),
- & MPI_UYZ,grad_shield(1,1),ivec_count(0),
+ & MPI_UYZ,grad_shieldbuf(1,1),ivec_count(0),
& ivec_displ(0),
& MPI_UYZ,FG_COMM,IERR)
call MPI_Allgatherv(grad_shield_side(1,1,ivec_start),
& ivec_count(fg_rank1),
- & MPI_SHI,grad_shield_side(1,1,1),ivec_count(0),
+ & MPI_SHI,grad_shield_sidebuf(1,1,1),ivec_count(0),
& ivec_displ(0),
& MPI_SHI,FG_COMM,IERR)
call MPI_Allgatherv(grad_shield_loc(1,1,ivec_start),
& ivec_count(fg_rank1),
- & MPI_SHI,grad_shield_loc(1,1,1),ivec_count(0),
+ & MPI_SHI,grad_shield_locbuf(1,1,1),ivec_count(0),
& ivec_displ(0),
& MPI_SHI,FG_COMM,IERR)
+ do i=1,nres
+ fac_shield(i)=fac_shieldbuf(i)
+ ishield_list(i)=ishield_listbuf(i)
+ do j=1,3
+ grad_shield(j,i)=grad_shieldbuf(j,i)
+ enddo !j
+ do j=1,ishield_list(i)
+ shield_list(j,i)=shield_listbuf(j,i)
+ do k=1,3
+ grad_shield_loc(k,j,i)=grad_shield_locbuf(k,j,i)
+ grad_shield_side(k,j,i)=grad_shield_sidebuf(k,j,i)
+ enddo !k
+ enddo !j
+ enddo !i
#ifdef DEBUG
write(iout,*) "after reduce fac_shield reduce"
do i=1,nres
call calctube(Etube)
elseif (TUBElog.eq.2) then
call calctube2(Etube)
+ elseif (TUBElog.eq.3) then
+ call calcnano(Etube)
else
Etube=0.0d0
endif
enddo
- enddo
+ enddo
+C j=1
+C i=0
+C print *,"KUPA2",gradbufc(j,i),wsc*gvdwc(j,i),
+C & wscp*gvdwc_scp(j,i),gvdwc_scpp(j,i),
+C & welec*gelc_long(j,i),wvdwpp*gvdwpp(j,i),
+C & wel_loc*gel_loc_long(j,i),
+C & wcorr*gradcorr_long(j,i),
+C & wcorr5*gradcorr5_long(j,i),
+C & wcorr6*gradcorr6_long(j,i),
+C & wturn6*gcorr6_turn_long(j,i),
+C & wstrain*ghpbc(j,i)
+C & ,wliptran*gliptranc(j,i)
+C & ,gradafm(j,i)
+C & ,welec*gshieldc(j,i)
+C & ,wcorr*gshieldc_ec(j,i)
+C & ,wturn3*gshieldc_t3(j,i)
+C & ,wturn4*gshieldc_t4(j,i)
+C & ,wel_loc*gshieldc_ll(j,i)
+C & ,wtube*gg_tube(j,i)
#else
do i=0,nct
do j=1,3
#ifdef TIMING
c time_allreduce=time_allreduce+MPI_Wtime()-time00
#endif
- do i=nnt,nres
+ do i=0,nres
do k=1,3
gradbufc(k,i)=0.0d0
enddo
enddo
- enddo
+ enddo
+C i=0
+C j=1
+C print *,"KUPA", gradbufc(j,i),welec*gelc(j,i),
+C & wel_loc*gel_loc(j,i),
+C & 0.5d0*wscp*gvdwc_scpp(j,i),
+C & welec*gelc_long(j,i),wvdwpp*gvdwpp(j,i),
+C & wel_loc*gel_loc_long(j,i),
+C & wcorr*gradcorr_long(j,i),
+C & wcorr5*gradcorr5_long(j,i),
+C & wcorr6*gradcorr6_long(j,i),
+C & wturn6*gcorr6_turn_long(j,i),
+C & wbond*gradb(j,i),
+C & wcorr*gradcorr(j,i),
+C & wturn3*gcorr3_turn(j,i),
+C & wturn4*gcorr4_turn(j,i),
+C & wcorr5*gradcorr5(j,i),
+C & wcorr6*gradcorr6(j,i),
+C & wturn6*gcorr6_turn(j,i),
+C & wsccor*gsccorc(j,i)
+C & ,wscloc*gscloc(j,i)
+C & ,wliptran*gliptranc(j,i)
+C & ,gradafm(j,i)
+C & +welec*gshieldc(j,i)
+C & +welec*gshieldc_loc(j,i)
+C & +wcorr*gshieldc_ec(j,i)
+C & +wcorr*gshieldc_loc_ec(j,i)
+C & +wturn3*gshieldc_t3(j,i)
+C & +wturn3*gshieldc_loc_t3(j,i)
+C & +wturn4*gshieldc_t4(j,i)
+C & ,wturn4*gshieldc_loc_t4(j,i)
+C & ,wel_loc*gshieldc_ll(j,i)
+C & ,wel_loc*gshieldc_loc_ll(j,i)
+C & ,wtube*gg_tube(j,i)
+
+C print *,gg_tube(1,0),"TU3"
#ifdef DEBUG
write (iout,*) "gloc before adding corr"
do i=1,4*nres
call MPI_Barrier(FG_COMM,IERR)
time_barrier_g=time_barrier_g+MPI_Wtime()-time00
time00=MPI_Wtime()
- call MPI_Reduce(gradbufc(1,1),gradc(1,1,icg),3*nres,
+ call MPI_Reduce(gradbufc(1,0),gradc(1,0,icg),3*nres+3,
& MPI_DOUBLE_PRECISION,MPI_SUM,king,FG_COMM,IERR)
call MPI_Reduce(gradbufx(1,1),gradx(1,1,icg),3*nres,
& MPI_DOUBLE_PRECISION,MPI_SUM,king,FG_COMM,IERR)
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),
if (ymedi.lt.0) ymedi=ymedi+boxysize
zmedi=mod(zmedi,boxzsize)
if (zmedi.lt.0) zmedi=zmedi+boxzsize
+ zmedi2=mod(zmedi,boxzsize)
+ if (zmedi2.lt.0) zmedi2=zmedi2+boxzsize
+ if ((zmedi2.gt.bordlipbot)
+ &.and.(zmedi2.lt.bordliptop)) then
+C the energy transfer exist
+ if (zmedi2.lt.buflipbot) then
+C what fraction I am in
+ fracinbuf=1.0d0-
+ & ((zmedi2-bordlipbot)/lipbufthick)
+C lipbufthick is thickenes of lipid buffore
+ sslipi=sscalelip(fracinbuf)
+ ssgradlipi=-sscagradlip(fracinbuf)/lipbufthick
+ elseif (zmedi2.gt.bufliptop) then
+ fracinbuf=1.0d0-((bordliptop-zmedi2)/lipbufthick)
+ sslipi=sscalelip(fracinbuf)
+ ssgradlipi=sscagradlip(fracinbuf)/lipbufthick
+ else
+ sslipi=1.0d0
+ ssgradlipi=0.0d0
+ endif
+ else
+ sslipi=0.0d0
+ ssgradlipi=0.0d0
+ endif
num_conti=0
call eelecij(i,i+2,ees,evdw1,eel_loc)
if (wturn3.gt.0.0d0) call eturn3(i,eello_turn3)
if (ymedi.lt.0) ymedi=ymedi+boxysize
zmedi=mod(zmedi,boxzsize)
if (zmedi.lt.0) zmedi=zmedi+boxzsize
-
+ zmedi2=mod(zmedi,boxzsize)
+ if (zmedi2.lt.0) zmedi2=zmedi2+boxzsize
+ if ((zmedi2.gt.bordlipbot)
+ &.and.(zmedi2.lt.bordliptop)) then
+C the energy transfer exist
+ if (zmedi2.lt.buflipbot) then
+C what fraction I am in
+ fracinbuf=1.0d0-
+ & ((zmedi2-bordlipbot)/lipbufthick)
+C lipbufthick is thickenes of lipid buffore
+ sslipi=sscalelip(fracinbuf)
+ ssgradlipi=-sscagradlip(fracinbuf)/lipbufthick
+ elseif (zmedi2.gt.bufliptop) then
+ fracinbuf=1.0d0-((bordliptop-zmedi2)/lipbufthick)
+ sslipi=sscalelip(fracinbuf)
+ ssgradlipi=sscagradlip(fracinbuf)/lipbufthick
+ else
+ sslipi=1.0d0
+ ssgradlipi=0.0
+ endif
+ else
+ sslipi=0.0d0
+ ssgradlipi=0.0
+ endif
num_conti=num_cont_hb(i)
c write(iout,*) "JESTEM W PETLI"
call eelecij(i,i+3,ees,evdw1,eel_loc)
if (ymedi.lt.0) ymedi=ymedi+boxysize
zmedi=mod(zmedi,boxzsize)
if (zmedi.lt.0) zmedi=zmedi+boxzsize
+ if ((zmedi.gt.bordlipbot)
+ &.and.(zmedi.lt.bordliptop)) then
+C the energy transfer exist
+ if (zmedi.lt.buflipbot) then
+C what fraction I am in
+ fracinbuf=1.0d0-
+ & ((zmedi-bordlipbot)/lipbufthick)
+C lipbufthick is thickenes of lipid buffore
+ sslipi=sscalelip(fracinbuf)
+ ssgradlipi=-sscagradlip(fracinbuf)/lipbufthick
+ elseif (zmedi.gt.bufliptop) then
+ fracinbuf=1.0d0-((bordliptop-zmedi)/lipbufthick)
+ sslipi=sscalelip(fracinbuf)
+ ssgradlipi=sscagradlip(fracinbuf)/lipbufthick
+ else
+ sslipi=1.0d0
+ ssgradlipi=0.0
+ endif
+ else
+ sslipi=0.0d0
+ ssgradlipi=0.0
+ endif
+C print *,sslipi,"TU?!"
C xmedi=xmedi+xshift*boxxsize
C ymedi=ymedi+yshift*boxysize
C zmedi=zmedi+zshift*boxzsize
zj=mod(zj,boxzsize)
if (zj.lt.0) zj=zj+boxzsize
if ((zj.lt.0).or.(xj.lt.0).or.(yj.lt.0)) write (*,*) "CHUJ"
+ if ((zj.gt.bordlipbot)
+ &.and.(zj.lt.bordliptop)) then
+C the energy transfer exist
+ if (zj.lt.buflipbot) then
+C what fraction I am in
+ fracinbuf=1.0d0-
+ & ((zj-bordlipbot)/lipbufthick)
+C lipbufthick is thickenes of lipid buffore
+ sslipj=sscalelip(fracinbuf)
+ ssgradlipj=-sscagradlip(fracinbuf)/lipbufthick
+ elseif (zj.gt.bufliptop) then
+ fracinbuf=1.0d0-((bordliptop-zj)/lipbufthick)
+ sslipj=sscalelip(fracinbuf)
+ ssgradlipj=sscagradlip(fracinbuf)/lipbufthick
+ else
+ sslipj=1.0d0
+ ssgradlipj=0.0
+ endif
+ else
+ sslipj=0.0d0
+ ssgradlipj=0.0
+ endif
dist_init=(xj-xmedi)**2+(yj-ymedi)**2+(zj-zmedi)**2
xj_safe=xj
yj_safe=yj
el2=el2*fac_shield(i)**2*fac_shield(j)**2
eesij=(el1+el2)
ees=ees+eesij
+C FOR NOW SHIELD IS NOT USED WITH LIPSCALE
+C & *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
else
fac_shield(i)=1.0
fac_shield(j)=1.0
eesij=(el1+el2)
ees=ees+eesij
+ &*((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
+C print *,"TUCC",(sslipi+sslipj)/2.0d0*lipscale**2+1.0d0
endif
evdw1=evdw1+evdwij*sss
+ & *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
+C print *,sslipi,sslipj,lipscale**2,
+C & (sslipi+sslipj)/2.0d0*lipscale**2+1.0d0
cd write(iout,'(2(2i3,2x),7(1pd12.4)/2(3(1pd12.4),5x)/)')
cd & iteli,i,itelj,j,aaa,bbb,ael6i,ael3i,
cd & 1.0D0/dsqrt(rrmij),evdwij,eesij,
C
#ifdef SPLITELE
facvdw=-6*rrmij*(ev1+evdwij)*sss
+ & *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
facel=-3*rrmij*(el1+eesij)
+ &*((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
fac1=fac
erij(1)=xj*rmij
erij(2)=yj*rmij
C & +grad_shield(k,j)*eesij/fac_shield(j)
enddo
C print *,"bafter", gelc_long(1,i), gelc_long(1,j)
+C Lipidic part for lipscale
+ gelc_long(3,j)=gelc_long(3,j)+
+ & ssgradlipj*eesij/2.0d0*lipscale**2
+
+ gelc_long(3,i)=gelc_long(3,i)+
+ & ssgradlipi*eesij/2.0d0*lipscale**2
*
* Loop over residues i+1 thru j-1.
cgrad enddo
if (sss.gt.0.0) then
ggg(1)=facvdw*xj+sssgrad*rmij*evdwij*xj
+ & *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
+
ggg(2)=facvdw*yj+sssgrad*rmij*evdwij*yj
+ & *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
+
ggg(3)=facvdw*zj+sssgrad*rmij*evdwij*zj
+ & *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
else
ggg(1)=0.0
ggg(2)=0.0
gvdwpp(k,j)=gvdwpp(k,j)+ggg(k)
gvdwpp(k,i)=gvdwpp(k,i)-ggg(k)
enddo
+C Lipidic part for scaling weight
+ gvdwpp(3,j)=gvdwpp(3,j)+
+ & sss*ssgradlipj*evdwij/2.0d0*lipscale**2
+ gvdwpp(3,i)=gvdwpp(3,i)+
+ & sss*ssgradlipi*evdwij/2.0d0*lipscale**2
+
*
* Loop over residues i+1 thru j-1.
*
#else
C MARYSIA
facvdw=(ev1+evdwij)*sss
+ & *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
facel=(el1+eesij)
fac1=fac
fac=-3*rrmij*(facvdw+facvdw+facel)
cgrad enddo
c 9/28/08 AL Gradient compotents will be summed only at the end
ggg(1)=facvdw*xj+sssgrad*rmij*evdwij*xj
+ & *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
+
ggg(2)=facvdw*yj+sssgrad*rmij*evdwij*yj
+ & *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
+
ggg(3)=facvdw*zj+sssgrad*rmij*evdwij*zj
+ & *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
do k=1,3
gvdwpp(k,j)=gvdwpp(k,j)+ggg(k)
gvdwpp(k,i)=gvdwpp(k,i)-ggg(k)
enddo
+ gvdwpp(3,j)=gvdwpp(3,j)+
+ & sss*ssgradlipj*evdwij/2.0d0*lipscale**2
+ gvdwpp(3,i)=gvdwpp(3,i)+
+ & sss*ssgradlipi*evdwij/2.0d0*lipscale**2
+
#endif
*
* Angular part
do k=1,3
ggg(k)=(ecosb*dcosb(k)+ecosg*dcosg(k))*
& fac_shield(i)**2*fac_shield(j)**2
+ & *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
enddo
c do k=1,3
c ghalf=0.5D0*ggg(k)
& +((ecosa*(dc_norm(k,j)-cosa*dc_norm(k,i))
& + ecosb*(erij(k)-cosb*dc_norm(k,i)))*vbld_inv(i+1))
& *fac_shield(i)**2*fac_shield(j)**2
+ & *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
gelc(k,j)=gelc(k,j)
& +((ecosa*(dc_norm(k,i)-cosa*dc_norm(k,j))
& + ecosg*(erij(k)-cosg*dc_norm(k,j)))*vbld_inv(j+1))
& *fac_shield(i)**2*fac_shield(j)**2
+ & *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
gelc_long(k,j)=gelc_long(k,j)+ggg(k)
gelc_long(k,i)=gelc_long(k,i)-ggg(k)
enddo
endif
eel_loc_ij=eel_loc_ij
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
C Now derivative over eel_loc
if ((fac_shield(i).gt.0).and.(fac_shield(j).gt.0).and.
& (shield_mode.gt.0)) then
& +a32*gmuij1(3)
& +a33*gmuij1(4))
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
c write(iout,*) "derivative over thatai"
c write(iout,*) a22*gmuij1(1), a23*gmuij1(2) ,a32*gmuij1(3),
c & a33*gmuij1(4)
gloc(nphi+i-1,icg)=gloc(nphi+i-1,icg)+
& geel_loc_ij*wel_loc
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
c Derivative over j residue
geel_loc_ji=a22*gmuji1(1)
gloc(nphi+j,icg)=gloc(nphi+j,icg)+
& geel_loc_ji*wel_loc
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
geel_loc_ji=
& +a22*gmuji2(1)
gloc(nphi+j-1,icg)=gloc(nphi+j-1,icg)+
& geel_loc_ji*wel_loc
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
#endif
cd write (iout,*) 'i',i,' j',j,' eel_loc_ij',eel_loc_ij
& (a22*muder(1,i)*mu(1,j)+a23*muder(1,i)*mu(2,j)
& +a32*muder(2,i)*mu(1,j)+a33*muder(2,i)*mu(2,j))
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
gel_loc_loc(j-1)=gel_loc_loc(j-1)+
& (a22*mu(1,i)*muder(1,j)+a23*mu(1,i)*muder(2,j)
& +a32*mu(2,i)*muder(1,j)+a33*mu(2,i)*muder(2,j))
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
C Derivatives of eello in DC(i+1) thru DC(j-1) or DC(nres-2)
do l=1,3
ggg(l)=(agg(l,1)*muij(1)+
& agg(l,2)*muij(2)+agg(l,3)*muij(3)+agg(l,4)*muij(4))
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
gel_loc_long(l,j)=gel_loc_long(l,j)+ggg(l)
gel_loc_long(l,i)=gel_loc_long(l,i)-ggg(l)
cgrad ghalf=0.5d0*ggg(l)
cgrad gel_loc(l,i)=gel_loc(l,i)+ghalf
cgrad gel_loc(l,j)=gel_loc(l,j)+ghalf
enddo
+ gel_loc_long(3,j)=gel_loc_long(3,j)+
+ & ssgradlipj*eel_loc_ij/2.0d0*lipscale/
+ & ((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
+ gel_loc_long(3,i)=gel_loc_long(3,i)+
+ & ssgradlipi*eel_loc_ij/2.0d0*lipscale/
+ & ((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
cgrad do k=i+1,j2
cgrad do l=1,3
cgrad gel_loc(l,k)=gel_loc(l,k)+ggg(l)
gel_loc(l,i)=gel_loc(l,i)+(aggi(l,1)*muij(1)+
& aggi(l,2)*muij(2)+aggi(l,3)*muij(3)+aggi(l,4)*muij(4))
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
gel_loc(l,i+1)=gel_loc(l,i+1)+(aggi1(l,1)*muij(1)+
& aggi1(l,2)*muij(2)+aggi1(l,3)*muij(3)+aggi1(l,4)*muij(4))
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
gel_loc(l,j)=gel_loc(l,j)+(aggj(l,1)*muij(1)+
& aggj(l,2)*muij(2)+aggj(l,3)*muij(3)+aggj(l,4)*muij(4))
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
gel_loc(l,j1)=gel_loc(l,j1)+(aggj1(l,1)*muij(1)+
& aggj1(l,2)*muij(2)+aggj1(l,3)*muij(3)+aggj1(l,4)*muij(4))
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
enddo
ENDIF
& dxi,dyi,dzi,dx_normi,dy_normi,dz_normi,xmedi,ymedi,zmedi,
& num_conti,j1,j2
j=i+2
-c write (iout,*) "eturn3",i,j,j1,j2
+C xj=(c(1,j)+c(1,j+1))/2.0d0
+C yj=(c(2,j)+c(2,j+1))/2.0d0
+ zj=(c(3,j)+c(3,j+1))/2.0d0
+C xj=mod(xj,boxxsize)
+C if (xj.lt.0) xj=xj+boxxsize
+C yj=mod(yj,boxysize)
+C if (yj.lt.0) yj=yj+boxysize
+ zj=mod(zj,boxzsize)
+ if (zj.lt.0) zj=zj+boxzsize
+ if ((zj.lt.0).or.(xj.lt.0).or.(yj.lt.0)) write (*,*) "CHUJ"
+ if ((zj.gt.bordlipbot)
+ &.and.(zj.lt.bordliptop)) then
+C the energy transfer exist
+ if (zj.lt.buflipbot) then
+C what fraction I am in
+ fracinbuf=1.0d0-
+ & ((zj-bordlipbot)/lipbufthick)
+C lipbufthick is thickenes of lipid buffore
+ sslipj=sscalelip(fracinbuf)
+ ssgradlipj=-sscagradlip(fracinbuf)/lipbufthick
+ elseif (zj.gt.bufliptop) then
+ fracinbuf=1.0d0-((bordliptop-zj)/lipbufthick)
+ sslipj=sscalelip(fracinbuf)
+ ssgradlipj=sscagradlip(fracinbuf)/lipbufthick
+ else
+ sslipj=1.0d0
+ ssgradlipj=0.0
+ endif
+ else
+ sslipj=0.0d0
+ ssgradlipj=0.0
+ endif
+C sslipj=0.0
+C ssgradlipj=0.0d0
+
+C write (iout,*) "eturn3",i,j,j1,j2
a_temp(1,1)=a22
a_temp(1,2)=a23
a_temp(2,1)=a32
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
+ fac_shield(i)=1.0d0
+ fac_shield(j)=1.0d0
C else
C fac_shield(i)=0.4
C fac_shield(j)=0.6
endif
C if (j.eq.78)
C & write(iout,*) i,j,fac_shield(i),fac_shield(j)
- eello_turn3=eello_turn3+0.5d0*(pizda(1,1)+pizda(2,2))
+ eello_turn3=eello_turn3+
+C & 1.0*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+ &0.5d0*(pizda(1,1)+pizda(2,2))
& *fac_shield(i)*fac_shield(j)
- eello_t3=0.5d0*(pizda(1,1)+pizda(2,2))
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+ eello_t3=
+ &0.5d0*(pizda(1,1)+pizda(2,2))
& *fac_shield(i)*fac_shield(j)
#ifdef NEWCORR
C Derivatives in theta
gloc(nphi+i,icg)=gloc(nphi+i,icg)
& +0.5d0*(gpizda1(1,1)+gpizda1(2,2))*wturn3
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
gloc(nphi+i+1,icg)=gloc(nphi+i+1,icg)
& +0.5d0*(gpizda2(1,1)+gpizda2(2,2))*wturn3
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
#endif
C if (energy_dec) write (iout,'(a6,2i5,0pf7.3)')
call matmat2(a_temp(1,1),auxmat3(1,1),pizda(1,1))
gel_loc_turn3(i)=gel_loc_turn3(i)+0.5d0*(pizda(1,1)+pizda(2,2))
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
C Derivatives in gamma(i+1)
call matmat2(EUg(1,1,i+1),EUgder(1,1,i+2),auxmat2(1,1))
call transpose2(auxmat2(1,1),auxmat3(1,1))
gel_loc_turn3(i+1)=gel_loc_turn3(i+1)
& +0.5d0*(pizda(1,1)+pizda(2,2))
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
C Cartesian derivatives
do l=1,3
c ghalf1=0.5d0*agg(l,1)
gcorr3_turn(l,i)=gcorr3_turn(l,i)
& +0.5d0*(pizda(1,1)+pizda(2,2))
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
a_temp(1,1)=aggi1(l,1)!+agg(l,1)
a_temp(1,2)=aggi1(l,2)!+agg(l,2)
gcorr3_turn(l,i+1)=gcorr3_turn(l,i+1)
& +0.5d0*(pizda(1,1)+pizda(2,2))
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
a_temp(1,1)=aggj(l,1)!+ghalf1
a_temp(1,2)=aggj(l,2)!+ghalf2
a_temp(2,1)=aggj(l,3)!+ghalf3
gcorr3_turn(l,j)=gcorr3_turn(l,j)
& +0.5d0*(pizda(1,1)+pizda(2,2))
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
a_temp(1,1)=aggj1(l,1)
a_temp(1,2)=aggj1(l,2)
a_temp(2,1)=aggj1(l,3)
gcorr3_turn(l,j1)=gcorr3_turn(l,j1)
& +0.5d0*(pizda(1,1)+pizda(2,2))
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
enddo
+ gshieldc_t3(3,i)=gshieldc_t3(3,i)+
+ & ssgradlipi*eello_t3/4.0d0*lipscale
+ gshieldc_t3(3,j)=gshieldc_t3(3,j)+
+ & ssgradlipj*eello_t3/4.0d0*lipscale
+ gshieldc_t3(3,i-1)=gshieldc_t3(3,i-1)+
+ & ssgradlipi*eello_t3/4.0d0*lipscale
+ gshieldc_t3(3,j-1)=gshieldc_t3(3,j-1)+
+ & ssgradlipj*eello_t3/4.0d0*lipscale
+
+C print *,ssgradlipi,ssgradlipj,eello_t3,sslipi,sslipj
return
end
C-------------------------------------------------------------------------------
cd call checkint_turn4(i,a_temp,eello_turn4_num)
c write (iout,*) "eturn4 i",i," j",j," j1",j1," j2",j2
c write(iout,*)"WCHODZE W PROGRAM"
+ zj=(c(3,j)+c(3,j+1))/2.0d0
+C xj=mod(xj,boxxsize)
+C if (xj.lt.0) xj=xj+boxxsize
+C yj=mod(yj,boxysize)
+C if (yj.lt.0) yj=yj+boxysize
+ zj=mod(zj,boxzsize)
+ if (zj.lt.0) zj=zj+boxzsize
+C if ((zj.lt.0).or.(xj.lt.0).or.(yj.lt.0)) write (*,*) "CHUJ"
+ if ((zj.gt.bordlipbot)
+ &.and.(zj.lt.bordliptop)) then
+C the energy transfer exist
+ if (zj.lt.buflipbot) then
+C what fraction I am in
+ fracinbuf=1.0d0-
+ & ((zj-bordlipbot)/lipbufthick)
+C lipbufthick is thickenes of lipid buffore
+ sslipj=sscalelip(fracinbuf)
+ ssgradlipj=-sscagradlip(fracinbuf)/lipbufthick
+ elseif (zj.gt.bufliptop) then
+ fracinbuf=1.0d0-((bordliptop-zj)/lipbufthick)
+ sslipj=sscalelip(fracinbuf)
+ ssgradlipj=sscagradlip(fracinbuf)/lipbufthick
+ else
+ sslipj=1.0d0
+ ssgradlipj=0.0
+ endif
+ else
+ sslipj=0.0d0
+ ssgradlipj=0.0
+ endif
+
a_temp(1,1)=a22
a_temp(1,2)=a23
a_temp(2,1)=a32
endif
eello_turn4=eello_turn4-(s1+s2+s3)
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
eello_t4=-(s1+s2+s3)
& *fac_shield(i)*fac_shield(j)
c write(iout,*)'chujOWO', auxvec(1),b1(1,iti2)
gloc(nphi+i,icg)=gloc(nphi+i,icg)
& -(gs13+gsE13+gsEE1)*wturn4
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
gloc(nphi+i+1,icg)= gloc(nphi+i+1,icg)
& -(gs23+gs21+gsEE2)*wturn4
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
gloc(nphi+i+2,icg)= gloc(nphi+i+2,icg)
& -(gs32+gsE31+gsEE3)*wturn4
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
c gloc(nphi+i+1,icg)=gloc(nphi+i+1,icg)-
c & gs2
s3=0.5d0*(pizda(1,1)+pizda(2,2))
gel_loc_turn4(i)=gel_loc_turn4(i)-(s1+s3)
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
C Derivatives in gamma(i+1)
call transpose2(EUgder(1,1,i+2),e2tder(1,1))
call matvec2(ae3(1,1),Ub2der(1,i+2),auxvec(1))
s3=0.5d0*(pizda(1,1)+pizda(2,2))
gel_loc_turn4(i+1)=gel_loc_turn4(i+1)-(s2+s3)
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
C Derivatives in gamma(i+2)
call transpose2(EUgder(1,1,i+3),e3tder(1,1))
call matvec2(e1a(1,1),Ub2der(1,i+3),auxvec(1))
s3=0.5d0*(pizda(1,1)+pizda(2,2))
gel_loc_turn4(i+2)=gel_loc_turn4(i+2)-(s1+s2+s3)
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
C Cartesian derivatives
C Derivatives of this turn contributions in DC(i+2)
if (j.lt.nres-1) then
ggg(l)=-(s1+s2+s3)
gcorr4_turn(l,i+2)=gcorr4_turn(l,i+2)-(s1+s2+s3)
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
enddo
endif
C Remaining derivatives of this turn contribution
s3=0.5d0*(pizda(1,1)+pizda(2,2))
gcorr4_turn(l,i)=gcorr4_turn(l,i)-(s1+s2+s3)
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
a_temp(1,1)=aggi1(l,1)
a_temp(1,2)=aggi1(l,2)
a_temp(2,1)=aggi1(l,3)
s3=0.5d0*(pizda(1,1)+pizda(2,2))
gcorr4_turn(l,i+1)=gcorr4_turn(l,i+1)-(s1+s2+s3)
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
a_temp(1,1)=aggj(l,1)
a_temp(1,2)=aggj(l,2)
a_temp(2,1)=aggj(l,3)
s3=0.5d0*(pizda(1,1)+pizda(2,2))
gcorr4_turn(l,j)=gcorr4_turn(l,j)-(s1+s2+s3)
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
a_temp(1,1)=aggj1(l,1)
a_temp(1,2)=aggj1(l,2)
a_temp(2,1)=aggj1(l,3)
c write (iout,*) "s1",s1," s2",s2," s3",s3," s1+s2+s3",s1+s2+s3
gcorr4_turn(l,j1)=gcorr4_turn(l,j1)-(s1+s2+s3)
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
enddo
+ gshieldc_t4(3,i)=gshieldc_t4(3,i)+
+ & ssgradlipi*eello_t4/4.0d0*lipscale
+ gshieldc_t4(3,j)=gshieldc_t4(3,j)+
+ & ssgradlipj*eello_t4/4.0d0*lipscale
+ gshieldc_t4(3,i-1)=gshieldc_t4(3,i-1)+
+ & ssgradlipi*eello_t4/4.0d0*lipscale
+ gshieldc_t4(3,j-1)=gshieldc_t4(3,j-1)+
+ & ssgradlipj*eello_t4/4.0d0*lipscale
return
end
C-----------------------------------------------------------------------------
else
do j=1,nbi
diff=vbld(i+nres)-vbldsc0(j,iti)
+ if (energy_dec) write (iout,*)
+ & "estr sc",i,iti,vbld(i+nres),vbldsc0(j,iti),diff,
+ & AKSC(j,iti),AKSC(j,iti)*diff*diff
ud(j)=aksc(j,iti)*diff
u(j)=abond0(j,iti)+0.5d0*ud(j)*diff
enddo
etheta=0.0D0
do i=ithet_start,ithet_end
c print *,i,itype(i-1),itype(i),itype(i-2)
+C if (itype(i-1).eq.ntyp1) cycle
if ((itype(i-1).eq.ntyp1).or.itype(i-2).eq.ntyp1
& .or.itype(i).eq.ntyp1) cycle
C print *,i,theta(i)
include 'COMMON.SBRIDGE'
double precision tub_r,vectube(3),enetube(maxres*2)
Etube=0.0d0
- do i=1,2*nres
+ do i=itube_start,itube_end
enetube(i)=0.0d0
+ enetube(i+nres)=0.0d0
enddo
C first we calculate the distance from tube center
C first sugare-phosphate group for NARES this would be peptide group
C for UNRES
- do i=1,nres
+ do i=itube_start,itube_end
C lets ommit dummy atoms for now
if ((itype(i).eq.ntyp1).or.(itype(i+1).eq.ntyp1)) cycle
C now calculate distance from center of tube and direction vectors
- vectube(1)=mod((c(1,i)+c(1,i+1))/2.0d0,boxxsize)
- if (vectube(1).lt.0) vectube(1)=vectube(1)+boxxsize
- vectube(2)=mod((c(2,i)+c(2,i+1))/2.0d0,boxysize)
- if (vectube(2).lt.0) vectube(2)=vectube(2)+boxysize
+ xmin=boxxsize
+ ymin=boxysize
+ do j=-1,1
+ vectube(1)=mod((c(1,i)+c(1,i+1))/2.0d0,boxxsize)
+ vectube(1)=vectube(1)+boxxsize*j
+ vectube(2)=mod((c(2,i)+c(2,i+1))/2.0d0,boxysize)
+ vectube(2)=vectube(2)+boxysize*j
+
+ xminact=abs(vectube(1)-tubecenter(1))
+ yminact=abs(vectube(2)-tubecenter(2))
+ if (xmin.gt.xminact) then
+ xmin=xminact
+ xtemp=vectube(1)
+ endif
+ if (ymin.gt.yminact) then
+ ymin=yminact
+ ytemp=vectube(2)
+ endif
+ enddo
+ vectube(1)=xtemp
+ vectube(2)=ytemp
vectube(1)=vectube(1)-tubecenter(1)
vectube(2)=vectube(2)-tubecenter(2)
C 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
+ 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+
+ 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
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 print *,gg_tube(1,0),"TU"
+
+
+ do i=itube_start,itube_end
C Lets not jump over memory as we use many times iti
iti=itype(i)
C lets ommit dummy atoms for now
C in UNRES uncomment the line below as GLY has no side-chain...
C .or.(iti.eq.10)
& ) cycle
- vectube(1)=c(1,i+nres)
- vectube(1)=mod(vectube(1),boxxsize)
- if (vectube(1).lt.0) vectube(1)=vectube(1)+boxxsize
- vectube(2)=c(2,i+nres)
- vectube(2)=mod(vectube(2),boxysize)
- if (vectube(2).lt.0) vectube(2)=vectube(2)+boxysize
-
+ xmin=boxxsize
+ ymin=boxysize
+ do j=-1,1
+ vectube(1)=mod((c(1,i+nres)),boxxsize)
+ vectube(1)=vectube(1)+boxxsize*j
+ vectube(2)=mod((c(2,i+nres)),boxysize)
+ vectube(2)=vectube(2)+boxysize*j
+
+ xminact=abs(vectube(1)-tubecenter(1))
+ yminact=abs(vectube(2)-tubecenter(2))
+ if (xmin.gt.xminact) then
+ xmin=xminact
+ xtemp=vectube(1)
+ endif
+ if (ymin.gt.yminact) then
+ ymin=yminact
+ ytemp=vectube(2)
+ endif
+ enddo
+ vectube(1)=xtemp
+ vectube(2)=ytemp
+C write(iout,*), "tututu", vectube(1),tubecenter(1),vectube(2),
+C & tubecenter(2)
vectube(1)=vectube(1)-tubecenter(1)
vectube(2)=vectube(2)-tubecenter(2)
C 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
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
+ 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+
+ 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(j,i-1)=gg_tube(j,i-1)+vectube(j)*fac
enddo
enddo
- do i=1,2*nres
- Etube=Etube+enetube(i)
+ do i=itube_start,itube_end
+ Etube=Etube+enetube(i)+enetube(i+nres)
enddo
C print *,"ETUBE", etube
return
include 'COMMON.SBRIDGE'
double precision tub_r,vectube(3),enetube(maxres*2)
Etube=0.0d0
- do i=1,2*nres
+ do i=itube_start,itube_end
enetube(i)=0.0d0
+ enetube(i+nres)=0.0d0
enddo
C first we calculate the distance from tube center
C first sugare-phosphate group for NARES this would be peptide group
C for UNRES
- do i=1,nres
+ do i=itube_start,itube_end
C lets ommit dummy atoms for now
if ((itype(i).eq.ntyp1).or.(itype(i+1).eq.ntyp1)) cycle
C now calculate distance from center of tube and direction vectors
- vectube(1)=mod((c(1,i)+c(1,i+1))/2.0d0,boxxsize)
- if (vectube(1).lt.0) vectube(1)=vectube(1)+boxxsize
- vectube(2)=mod((c(2,i)+c(2,i+1))/2.0d0,boxysize)
- if (vectube(2).lt.0) vectube(2)=vectube(2)+boxysize
+C vectube(1)=mod((c(1,i)+c(1,i+1))/2.0d0,boxxsize)
+C if (vectube(1).lt.0) vectube(1)=vectube(1)+boxxsize
+C vectube(2)=mod((c(2,i)+c(2,i+1))/2.0d0,boxysize)
+C if (vectube(2).lt.0) vectube(2)=vectube(2)+boxysize
+ xmin=boxxsize
+ ymin=boxysize
+ do j=-1,1
+ vectube(1)=mod((c(1,i)+c(1,i+1))/2.0d0,boxxsize)
+ vectube(1)=vectube(1)+boxxsize*j
+ vectube(2)=mod((c(2,i)+c(2,i+1))/2.0d0,boxysize)
+ vectube(2)=vectube(2)+boxysize*j
+
+ xminact=abs(vectube(1)-tubecenter(1))
+ yminact=abs(vectube(2)-tubecenter(2))
+ if (xmin.gt.xminact) then
+ xmin=xminact
+ xtemp=vectube(1)
+ endif
+ if (ymin.gt.yminact) then
+ ymin=yminact
+ ytemp=vectube(2)
+ endif
+ enddo
+ vectube(1)=xtemp
+ vectube(2)=ytemp
vectube(1)=vectube(1)-tubecenter(1)
vectube(2)=vectube(2)-tubecenter(2)
rdiff=tub_r-tubeR0
C and its 6 power
rdiff6=rdiff**6.0d0
+C THIS FRAGMENT MAKES TUBE FINITE
+ positi=mod((c(3,i)+c(3,i+1))/2.0d0,boxzsize)
+ if (positi.le.0) positi=positi+boxzsize
+C print *,mod(c(3,i+nres),boxzsize),bordlipbot,bordliptop
+c for each residue check if it is in lipid or lipid water border area
+C respos=mod(c(3,i+nres),boxzsize)
+ print *,positi,bordtubebot,buftubebot,bordtubetop
+ if ((positi.gt.bordtubebot)
+ & .and.(positi.lt.bordtubetop)) then
+C the energy transfer exist
+ if (positi.lt.buftubebot) then
+ fracinbuf=1.0d0-
+ & ((positi-bordtubebot)/tubebufthick)
+C lipbufthick is thickenes of lipid buffore
+ sstube=sscalelip(fracinbuf)
+ ssgradtube=-sscagradlip(fracinbuf)/tubebufthick
+ print *,ssgradtube, sstube,tubetranene(itype(i))
+ enetube(i)=enetube(i)+sstube*tubetranenepep
+C gg_tube_SC(3,i)=gg_tube_SC(3,i)
+C &+ssgradtube*tubetranene(itype(i))
+C gg_tube(3,i-1)= gg_tube(3,i-1)
+C &+ssgradtube*tubetranene(itype(i))
+C print *,"doing sccale for lower part"
+ elseif (positi.gt.buftubetop) then
+ fracinbuf=1.0d0-
+ &((bordtubetop-positi)/tubebufthick)
+ sstube=sscalelip(fracinbuf)
+ ssgradtube=sscagradlip(fracinbuf)/tubebufthick
+ enetube(i)=enetube(i)+sstube*tubetranenepep
+C gg_tube_SC(3,i)=gg_tube_SC(3,i)
+C &+ssgradtube*tubetranene(itype(i))
+C gg_tube(3,i-1)= gg_tube(3,i-1)
+C &+ssgradtube*tubetranene(itype(i))
+C print *, "doing sscalefor top part",sslip,fracinbuf
+ else
+ sstube=1.0d0
+ ssgradtube=0.0d0
+ enetube(i)=enetube(i)+sstube*tubetranenepep
+C print *,"I am in true lipid"
+ endif
+ else
+C sstube=0.0d0
+C ssgradtube=0.0d0
+ cycle
+ endif ! if in lipid or buffor
+
C for vectorization reasons we will sumup at the end to avoid depenence of previous
- enetube(i)=pep_aa_tube/rdiff6**2.0d0-pep_bb_tube/rdiff6
+ enetube(i)=enetube(i)+sstube*
+ &(pep_aa_tube/rdiff6**2.0d0+pep_bb_tube/rdiff6)
C write(iout,*) "TU13",i,rdiff6,enetube(i)
C print *,rdiff,rdiff6,pep_aa_tube
C pep_aa_tube and pep_bb_tube are precomputed values A=4eps*sigma^12 B=4eps*sigma^6
C now we calculate gradient
- fac=(-12.0d0*pep_aa_tube/rdiff6+
- & 6.0d0*pep_bb_tube)/rdiff6/rdiff
+ fac=(-12.0d0*pep_aa_tube/rdiff6-
+ & 6.0d0*pep_bb_tube)/rdiff6/rdiff*sstube
C write(iout,'(a5,i4,f12.1,3f12.5)') "TU13",i,rdiff6,enetube(i),
C &rdiff,fac
gg_tube(j,i-1)=gg_tube(j,i-1)+vectube(j)*fac/2.0d0
gg_tube(j,i)=gg_tube(j,i)+vectube(j)*fac/2.0d0
enddo
+ gg_tube(3,i)=gg_tube(3,i)
+ &+ssgradtube*enetube(i)/sstube/2.0d0
+ gg_tube(3,i-1)= gg_tube(3,i-1)
+ &+ssgradtube*enetube(i)/sstube/2.0d0
+
enddo
C basically thats all code now we split for side-chains (REMEMBER to sum up at the END)
- do i=1,nres
+C print *,gg_tube(1,0),"TU"
+ do i=itube_start,itube_end
C Lets not jump over memory as we use many times iti
iti=itype(i)
C lets ommit dummy atoms for now
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)
+ enetube(i+nres)=(sc_aa_tube/rdiff6**2.0d0+sc_bb_tube/rdiff6)
& *sstube+enetube(i+nres)
C pep_aa_tube and pep_bb_tube are precomputed values A=4eps*sigma^12 B=4eps*sigma^6
C now we calculate gradient
- fac=(-12.0d0*sc_aa_tube/rdiff6**2.0d0/rdiff+
+ fac=(-12.0d0*sc_aa_tube/rdiff6**2.0d0/rdiff-
& 6.0d0*sc_bb_tube/rdiff6/rdiff)*sstube
C now direction of gg_tube vector
do j=1,3
&+ssgradtube*enetube(i+nres)/sstube
enddo
- do i=1,2*nres
- Etube=Etube+enetube(i)
+ do i=itube_start,itube_end
+ Etube=Etube+enetube(i)+enetube(i+nres)
+ enddo
+C print *,"ETUBE", etube
+ return
+ end
+C TO DO 1) add to total energy
+C 2) add to gradient summation
+C 3) add reading parameters (AND of course oppening of PARAM file)
+C 4) add reading the center of tube
+C 5) add COMMONs
+C 6) add to zerograd
+
+
+C#-------------------------------------------------------------------------------
+C This subroutine is to mimic the histone like structure but as well can be
+C utilizet to nanostructures (infinit) small modification has to be used to
+C make it finite (z gradient at the ends has to be changes as well as the x,y
+C gradient has to be modified at the ends
+C The energy function is Kihara potential
+C E=4esp*((sigma/(r-r0))^12 - (sigma/(r-r0))^6)
+C 4eps is depth of well sigma is r_minimum r is distance from center of tube
+C and r0 is the excluded size of nanotube (can be set to 0 if we want just a
+C simple Kihara potential
+ subroutine calcnano(Etube)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.LOCAL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.NAMES'
+ include 'COMMON.INTERACT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CALC'
+ include 'COMMON.CONTROL'
+ include 'COMMON.SPLITELE'
+ include 'COMMON.SBRIDGE'
+ double precision tub_r,vectube(3),enetube(maxres*2),
+ & enecavtube(maxres*2)
+ Etube=0.0d0
+ do i=itube_start,itube_end
+ enetube(i)=0.0d0
+ enetube(i+nres)=0.0d0
+ enddo
+C first we calculate the distance from tube center
+C first sugare-phosphate group for NARES this would be peptide group
+C for UNRES
+ do i=itube_start,itube_end
+C lets ommit dummy atoms for now
+ if ((itype(i).eq.ntyp1).or.(itype(i+1).eq.ntyp1)) cycle
+C now calculate distance from center of tube and direction vectors
+ xmin=boxxsize
+ ymin=boxysize
+ zmin=boxzsize
+
+ do j=-1,1
+ vectube(1)=mod((c(1,i)+c(1,i+1))/2.0d0,boxxsize)
+ vectube(1)=vectube(1)+boxxsize*j
+ vectube(2)=mod((c(2,i)+c(2,i+1))/2.0d0,boxysize)
+ vectube(2)=vectube(2)+boxysize*j
+ vectube(3)=mod((c(3,i)+c(3,i+1))/2.0d0,boxzsize)
+ vectube(3)=vectube(3)+boxzsize*j
+
+
+ xminact=abs(vectube(1)-tubecenter(1))
+ yminact=abs(vectube(2)-tubecenter(2))
+ zminact=abs(vectube(3)-tubecenter(3))
+
+ if (xmin.gt.xminact) then
+ xmin=xminact
+ xtemp=vectube(1)
+ endif
+ if (ymin.gt.yminact) then
+ ymin=yminact
+ ytemp=vectube(2)
+ endif
+ if (zmin.gt.zminact) then
+ zmin=zminact
+ ztemp=vectube(3)
+ endif
+ enddo
+ vectube(1)=xtemp
+ vectube(2)=ytemp
+ vectube(3)=ztemp
+
+ vectube(1)=vectube(1)-tubecenter(1)
+ vectube(2)=vectube(2)-tubecenter(2)
+ vectube(3)=vectube(3)-tubecenter(3)
+
+C print *,"x",(c(1,i)+c(1,i+1))/2.0d0,tubecenter(1)
+C print *,"y",(c(2,i)+c(2,i+1))/2.0d0,tubecenter(2)
+C as the tube is infinity we do not calculate the Z-vector use of Z
+C as chosen axis
+C vectube(3)=0.0d0
+C now calculte the distance
+ tub_r=dsqrt(vectube(1)**2+vectube(2)**2+vectube(3)**2)
+C now normalize vector
+ vectube(1)=vectube(1)/tub_r
+ vectube(2)=vectube(2)/tub_r
+ vectube(3)=vectube(3)/tub_r
+C calculte rdiffrence between r and r0
+ rdiff=tub_r-tubeR0
+C and its 6 power
+ rdiff6=rdiff**6.0d0
+C for vectorization reasons we will sumup at the end to avoid depenence of previous
+ enetube(i)=pep_aa_tube/rdiff6**2.0d0+pep_bb_tube/rdiff6
+C write(iout,*) "TU13",i,rdiff6,enetube(i)
+C print *,rdiff,rdiff6,pep_aa_tube
+C pep_aa_tube and pep_bb_tube are precomputed values A=4eps*sigma^12 B=4eps*sigma^6
+C now we calculate gradient
+ fac=(-12.0d0*pep_aa_tube/rdiff6-
+ & 6.0d0*pep_bb_tube)/rdiff6/rdiff
+C write(iout,'(a5,i4,f12.1,3f12.5)') "TU13",i,rdiff6,enetube(i),
+C &rdiff,fac
+ if (acavtubpep.eq.0.0d0) then
+C go to 667
+ enecavtube(i)=0.0
+ faccav=0.0
+ else
+ denominator=(1.0+dcavtubpep*rdiff6*rdiff6)
+ enecavtube(i)=
+ & (bcavtubpep*rdiff+acavtubpep*sqrt(rdiff)+ccavtubpep)
+ & /denominator
+ enecavtube(i)=0.0
+ faccav=((bcavtubpep*1.0d0+acavtubpep/2.0d0/sqrt(rdiff))
+ & *denominator-(bcavtubpep*rdiff+acavtubpep*sqrt(rdiff)
+ & +ccavtubpep)*rdiff6**2.0d0/rdiff*dcavtubpep*12.0d0)
+ & /denominator**2.0d0
+C faccav=0.0
+C fac=fac+faccav
+C 667 continue
+ endif
+C print *,"TUT",i,iti,rdiff,rdiff6,acavtubpep,denominator,
+C & enecavtube(i),faccav
+C print *,"licz=",
+C & (bcavtub(iti)*rdiff+acavtub(iti)*sqrt(rdiff)+ccavtub(iti))
+CX print *,"finene=",enetube(i+nres)+enecavtube(i)
+
+C now direction of gg_tube vector
+ do j=1,3
+ gg_tube(j,i-1)=gg_tube(j,i-1)+vectube(j)*fac/2.0d0
+ gg_tube(j,i)=gg_tube(j,i)+vectube(j)*fac/2.0d0
+ enddo
+ enddo
+
+ do i=itube_start,itube_end
+ enecavtube(i)=0.0
+C Lets not jump over memory as we use many times iti
+ iti=itype(i)
+C lets ommit dummy atoms for now
+ if ((iti.eq.ntyp1)
+C in UNRES uncomment the line below as GLY has no side-chain...
+C .or.(iti.eq.10)
+ & ) cycle
+ xmin=boxxsize
+ ymin=boxysize
+ zmin=boxzsize
+ do j=-1,1
+ vectube(1)=mod((c(1,i+nres)),boxxsize)
+ vectube(1)=vectube(1)+boxxsize*j
+ vectube(2)=mod((c(2,i+nres)),boxysize)
+ vectube(2)=vectube(2)+boxysize*j
+ vectube(3)=mod((c(3,i+nres)),boxzsize)
+ vectube(3)=vectube(3)+boxzsize*j
+
+
+ xminact=abs(vectube(1)-tubecenter(1))
+ yminact=abs(vectube(2)-tubecenter(2))
+ zminact=abs(vectube(3)-tubecenter(3))
+
+ if (xmin.gt.xminact) then
+ xmin=xminact
+ xtemp=vectube(1)
+ endif
+ if (ymin.gt.yminact) then
+ ymin=yminact
+ ytemp=vectube(2)
+ endif
+ if (zmin.gt.zminact) then
+ zmin=zminact
+ ztemp=vectube(3)
+ endif
+ enddo
+ vectube(1)=xtemp
+ vectube(2)=ytemp
+ vectube(3)=ztemp
+
+C write(iout,*), "tututu", vectube(1),tubecenter(1),vectube(2),
+C & tubecenter(2)
+ vectube(1)=vectube(1)-tubecenter(1)
+ vectube(2)=vectube(2)-tubecenter(2)
+ vectube(3)=vectube(3)-tubecenter(3)
+C now calculte the distance
+ tub_r=dsqrt(vectube(1)**2+vectube(2)**2+vectube(3)**2)
+C now normalize vector
+ vectube(1)=vectube(1)/tub_r
+ vectube(2)=vectube(2)/tub_r
+ vectube(3)=vectube(3)/tub_r
+
+C calculte rdiffrence between r and r0
+ rdiff=tub_r-tubeR0
+C and its 6 power
+ rdiff6=rdiff**6.0d0
+C for vectorization reasons we will sumup at the end to avoid depenence of previous
+ sc_aa_tube=sc_aa_tube_par(iti)
+ sc_bb_tube=sc_bb_tube_par(iti)
+ enetube(i+nres)=sc_aa_tube/rdiff6**2.0d0+sc_bb_tube/rdiff6
+C enetube(i+nres)=0.0d0
+C pep_aa_tube and pep_bb_tube are precomputed values A=4eps*sigma^12 B=4eps*sigma^6
+C now we calculate gradient
+ fac=-12.0d0*sc_aa_tube/rdiff6**2.0d0/rdiff-
+ & 6.0d0*sc_bb_tube/rdiff6/rdiff
+C fac=0.0
+C now direction of gg_tube vector
+C Now cavity term E=a(x+bsqrt(x)+c)/(1+dx^12)
+ if (acavtub(iti).eq.0.0d0) then
+C go to 667
+ enecavtube(i+nres)=0.0
+ faccav=0.0
+ else
+ denominator=(1.0+dcavtub(iti)*rdiff6*rdiff6)
+ enecavtube(i+nres)=
+ & (bcavtub(iti)*rdiff+acavtub(iti)*sqrt(rdiff)+ccavtub(iti))
+ & /denominator
+C enecavtube(i)=0.0
+ faccav=((bcavtub(iti)*1.0d0+acavtub(iti)/2.0d0/sqrt(rdiff))
+ & *denominator-(bcavtub(iti)*rdiff+acavtub(iti)*sqrt(rdiff)
+ & +ccavtub(iti))*rdiff6**2.0d0/rdiff*dcavtub(iti)*12.0d0)
+ & /denominator**2.0d0
+C faccav=0.0
+ fac=fac+faccav
+C 667 continue
+ endif
+C print *,"TUT",i,iti,rdiff,rdiff6,acavtub(iti),denominator,
+C & enecavtube(i),faccav
+C print *,"licz=",
+C & (bcavtub(iti)*rdiff+acavtub(iti)*sqrt(rdiff)+ccavtub(iti))
+C print *,"finene=",enetube(i+nres)+enecavtube(i)
+ do j=1,3
+ gg_tube_SC(j,i)=gg_tube_SC(j,i)+vectube(j)*fac
+ gg_tube(j,i-1)=gg_tube(j,i-1)+vectube(j)*fac
+ enddo
+ enddo
+C Now cavity term E=a(x+bsqrt(x)+c)/(1+dx^12)
+C do i=itube_start,itube_end
+C enecav(i)=0.0
+C iti=itype(i)
+C if (acavtub(iti).eq.0.0) cycle
+
+
+
+ do i=itube_start,itube_end
+ Etube=Etube+enetube(i)+enetube(i+nres)+enecavtube(i)
+ & +enecavtube(i+nres)
enddo
C print *,"ETUBE", etube
return
projects / unres.git / blobdiff