call set_shield_fac2
endif
call eelec(ees,evdw1,eel_loc,eello_turn3,eello_turn4)
-C write(iout,*) 'po eelec'
+c write(iout,*) 'po eelec eello_turn4',eello_turn4
C Calculate excluded-volume interaction energy between peptide groups
C and side chains.
call multibody_hb(ecorr,ecorr5,ecorr6,n_corr,n_corr1)
endif
#endif
+c write (iout,*) "nsaxs",nsaxs
c write (iout,*) "From Esaxs: Esaxs_constr",Esaxs_constr
if (nsaxs.gt.0 .and. saxs_mode.eq.0) then
call e_saxs(Esaxs_constr)
edfabet=0.0d0
if (wdfa_beta.gt.0) call edfab(edfabet)
c write(iout,*)'edfab is finished!', wdfa_beta,edfabet
+#else
+ edfadis=0.0d0
+ edfator=0.0d0
+ edfanei=0.0d0
+ edfabet=0.0d0
#endif
-
c write (iout,*) "ft(6)",fact(6)," evdw",evdw," evdw_t",evdw_t
#ifdef SPLITELE
if (shield_mode.gt.0) then
edfator = energia(29)
edfanei = energia(30)
edfabet = energia(31)
+ Eafmforc=0.0d0
+ etube=0.0d0
+ Uconst=0.0d0
#ifdef SPLITELE
write(iout,10) evdw,wsc,evdw2,wscp,ees,welec*fact(1),evdw1,wvdwpp,
& estr,wbond,ebe,wang,escloc,wscloc,etors,wtor*fact(1),
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
+ call to_box(xi,yi,zi)
C Change 12/1/95
num_conti=0
C
xj=c(1,nres+j)-xi
yj=c(2,nres+j)-yi
zj=c(3,nres+j)-zi
+ call to_box(xj,yj,zj)
+ xj=boxshift(xj-xi,boxxsize)
+ yj=boxshift(yj-yi,boxysize)
+ zj=boxshift(zj-zi,boxzsize)
C Change 12/1/95 to calculate four-body interactions
rij=xj*xj+yj*yj+zj*zj
rrij=1.0D0/rij
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
+ call to_box(xi,yi,zi)
C
C Calculate SC interaction energy.
C
xj=c(1,nres+j)-xi
yj=c(2,nres+j)-yi
zj=c(3,nres+j)-zi
+ call to_box(xj,yj,zj)
+ xj=boxshift(xj-xi,boxxsize)
+ yj=boxshift(yj-yi,boxysize)
+ zj=boxshift(zj-zi,boxzsize)
rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
fac_augm=rrij**expon
e_augm=augm(itypi,itypj)*fac_augm
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
+ call to_box(xi,yi,zi)
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
+ xj=c(1,nres+j)
+ yj=c(2,nres+j)
+ zj=c(3,nres+j)
+ call to_box(xj,yj,zj)
+ xj=boxshift(xj-xi,boxxsize)
+ yj=boxshift(yj-yi,boxysize)
+ zj=boxshift(zj-zi,boxzsize)
dxj=dc_norm(1,nres+j)
dyj=dc_norm(2,nres+j)
dzj=dc_norm(3,nres+j)
yi=c(2,nres+i)
zi=c(3,nres+i)
C returning the ith atom to box
- 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
- 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
-
+ call to_box(xi,yi,zi)
+ call lipid_layer(xi,yi,zi,sslipi,ssgradlipi)
dxi=dc_norm(1,nres+i)
dyi=dc_norm(2,nres+i)
dzi=dc_norm(3,nres+i)
yj=c(2,nres+j)
zj=c(3,nres+j)
C returning jth atom to box
- 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)) then
-
-C write(iout,*) "tu,", i,j,aa_aq(itypi,itypj)-aa,
-C & bb_aq(itypi,itypj)-bb,
-C & sslipi,sslipj
-C endif
-
-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
- yj_safe=yj
- zj_safe=zj
- subchap=0
-C finding the closest
- 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
-
+ call to_box(xj,yj,zj)
+ call lipid_layer(xj,yj,zj,sslipj,ssgradlipj)
+ 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(iout,'(2e15.5)')
+c &(aa-aa_aq(itypi,itypj)),(bb-bb_aq(itypi,itypj))
+ xj=boxshift(xj-xi,boxxsize)
+ yj=boxshift(yj-yi,boxysize)
+ zj=boxshift(zj-zi,boxzsize)
dxj=dc_norm(1,nres+j)
dyj=dc_norm(2,nres+j)
dzj=dc_norm(3,nres+j)
#endif
c#undef DEBUG
c endif
- if (energy_dec) write (iout,'(a,2i5,3f10.5)')
- & 'r sss evdw',i,j,1.0d0/rij,sss,evdwij
+ if (energy_dec) write (iout,'(a,2i5,4f10.5,e15.5)')
+ & 'r sss evdw',i,j,1.0d0/rij,sss,sslipi,sslipj,evdwij
if (calc_grad) then
C Calculate gradient components.
e1=e1*eps1*eps2rt**2*eps3rt**2
fac=rij*fac
fac=fac+evdwij/sss*sssgrad/sigma(itypi,itypj)*rij
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
gg(1)=xj*fac
gg(2)=yj*fac
gg(3)=zj*fac
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
+ call to_box(xi,yi,zi)
+ call lipid_layer(xi,yi,zi,sslipi,ssgradlipi)
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
+ xj=c(1,nres+j)
+ yj=c(2,nres+j)
+ zj=c(3,nres+j)
+ call to_box(xj,yj,zj)
+ call lipid_layer(xj,yj,zj,sslipj,ssgradlipj)
+ 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
+ xj=boxshift(xj-xi,boxxsize)
+ yj=boxshift(yj-yi,boxysize)
+ zj=boxshift(zj-zi,boxzsize)
dxj=dc_norm(1,nres+j)
dyj=dc_norm(2,nres+j)
dzj=dc_norm(3,nres+j)
fac=rij*fac-2*expon*rrij*e_augm
fac=fac+(evdwij+e_augm)*sssgrad/sss*rij
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
gg(1)=xj*fac
gg(2)=yj*fac
gg(3)=zj*fac
common /locel/ a_temp,agg,aggi,aggi1,aggj,aggj1,a22,a23,a32,a33,
& dxi,dyi,dzi,dx_normi,dy_normi,dz_normi,xmedi,ymedi,zmedi,
& num_conti,j1,j2
+ double precision sslipi,sslipj,ssgradlipi,ssgradlipj
+ common /lipcalc/ sslipi,sslipj,ssgradlipi,ssgradlipj
c 4/26/02 - AL scaling factor for 1,4 repulsive VDW interactions
#ifdef MOMENT
double precision scal_el /1.0d0/
xmedi=c(1,i)+0.5d0*dxi
ymedi=c(2,i)+0.5d0*dyi
zmedi=c(3,i)+0.5d0*dzi
- xmedi=mod(xmedi,boxxsize)
- if (xmedi.lt.0) xmedi=xmedi+boxxsize
- ymedi=mod(ymedi,boxysize)
- if (ymedi.lt.0) ymedi=ymedi+boxysize
- zmedi=mod(zmedi,boxzsize)
- if (zmedi.lt.0) zmedi=zmedi+boxzsize
+ call to_box(xmedi,ymedi,zmedi)
+ call lipid_layer(xmedi,ymedi,zmedi,sslipi,ssgradlipi)
num_conti=0
call eelecij(i,i+2,ees,evdw1,eel_loc)
if (wturn3.gt.0.0d0) call eturn3(i,eello_turn3)
xmedi=c(1,i)+0.5d0*dxi
ymedi=c(2,i)+0.5d0*dyi
zmedi=c(3,i)+0.5d0*dzi
-C Return atom into box, boxxsize is size of box in x dimension
-c 194 continue
-c if (xmedi.gt.((0.5d0)*boxxsize)) xmedi=xmedi-boxxsize
-c if (xmedi.lt.((-0.5d0)*boxxsize)) xmedi=xmedi+boxxsize
-C Condition for being inside the proper box
-c if ((xmedi.gt.((0.5d0)*boxxsize)).or.
-c & (xmedi.lt.((-0.5d0)*boxxsize))) then
-c go to 194
-c endif
-c 195 continue
-c if (ymedi.gt.((0.5d0)*boxysize)) ymedi=ymedi-boxysize
-c if (ymedi.lt.((-0.5d0)*boxysize)) ymedi=ymedi+boxysize
-C Condition for being inside the proper box
-c if ((ymedi.gt.((0.5d0)*boxysize)).or.
-c & (ymedi.lt.((-0.5d0)*boxysize))) then
-c go to 195
-c endif
-c 196 continue
-c if (zmedi.gt.((0.5d0)*boxzsize)) zmedi=zmedi-boxzsize
-c if (zmedi.lt.((-0.5d0)*boxzsize)) zmedi=zmedi+boxzsize
-C Condition for being inside the proper box
-c if ((zmedi.gt.((0.5d0)*boxzsize)).or.
-c & (zmedi.lt.((-0.5d0)*boxzsize))) then
-c go to 196
-c endif
- xmedi=mod(xmedi,boxxsize)
- if (xmedi.lt.0) xmedi=xmedi+boxxsize
- ymedi=mod(ymedi,boxysize)
- if (ymedi.lt.0) ymedi=ymedi+boxysize
- zmedi=mod(zmedi,boxzsize)
- if (zmedi.lt.0) zmedi=zmedi+boxzsize
+ call to_box(xmedi,ymedi,zmedi)
+ call lipid_layer(xmedi,ymedi,zmedi,sslipi,ssgradlipi)
#ifdef FOURBODY
num_conti=num_cont_hb(i)
#endif
call eelecij(i,i+3,ees,evdw1,eel_loc)
if (wturn4.gt.0.0d0 .and. itype(i+2).ne.ntyp1)
& call eturn4(i,eello_turn4)
+c write (iout,*) "i",i," eello_turn4",eello_turn4
#ifdef FOURBODY
num_cont_hb(i)=num_conti
#endif
xmedi=c(1,i)+0.5d0*dxi
ymedi=c(2,i)+0.5d0*dyi
zmedi=c(3,i)+0.5d0*dzi
- xmedi=mod(xmedi,boxxsize)
- if (xmedi.lt.0) xmedi=xmedi+boxxsize
- ymedi=mod(ymedi,boxysize)
- if (ymedi.lt.0) ymedi=ymedi+boxysize
- zmedi=mod(zmedi,boxzsize)
- if (zmedi.lt.0) zmedi=zmedi+boxzsize
-C xmedi=xmedi+xshift*boxxsize
-C ymedi=ymedi+yshift*boxysize
-C zmedi=zmedi+zshift*boxzsize
-
-C Return tom into box, boxxsize is size of box in x dimension
-c 164 continue
-c if (xmedi.gt.((xshift+0.5d0)*boxxsize)) xmedi=xmedi-boxxsize
-c if (xmedi.lt.((xshift-0.5d0)*boxxsize)) xmedi=xmedi+boxxsize
-C Condition for being inside the proper box
-c if ((xmedi.gt.((xshift+0.5d0)*boxxsize)).or.
-c & (xmedi.lt.((xshift-0.5d0)*boxxsize))) then
-c go to 164
-c endif
-c 165 continue
-c if (ymedi.gt.((yshift+0.5d0)*boxysize)) ymedi=ymedi-boxysize
-c if (ymedi.lt.((yshift-0.5d0)*boxysize)) ymedi=ymedi+boxysize
-C Condition for being inside the proper box
-c if ((ymedi.gt.((yshift+0.5d0)*boxysize)).or.
-c & (ymedi.lt.((yshift-0.5d0)*boxysize))) then
-c go to 165
-c endif
-c 166 continue
-c if (zmedi.gt.((zshift+0.5d0)*boxzsize)) zmedi=zmedi-boxzsize
-c if (zmedi.lt.((zshift-0.5d0)*boxzsize)) zmedi=zmedi+boxzsize
-cC Condition for being inside the proper box
-c if ((zmedi.gt.((zshift+0.5d0)*boxzsize)).or.
-c & (zmedi.lt.((zshift-0.5d0)*boxzsize))) then
-c go to 166
-c endif
-
-c write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i)
+ call to_box(xmedi,ymedi,zmedi)
+ call lipid_layer(xmedi,ymedi,zmedi,sslipi,ssgradlipi)
#ifdef FOURBODY
num_conti=num_cont_hb(i)
#endif
common /locel/ a_temp,agg,aggi,aggi1,aggj,aggj1,a22,a23,a32,a33,
& dxi,dyi,dzi,dx_normi,dy_normi,dz_normi,xmedi,ymedi,zmedi,
& num_conti,j1,j2
+ double precision sslipi,sslipj,ssgradlipi,ssgradlipj,faclipij,
+ & faclipij2
+ common /lipcalc/ sslipi,sslipj,ssgradlipi,ssgradlipj,faclipij
c 4/26/02 - AL scaling factor for 1,4 repulsive VDW interactions
#ifdef MOMENT
double precision scal_el /1.0d0/
xj=c(1,j)+0.5D0*dxj
yj=c(2,j)+0.5D0*dyj
zj=c(3,j)+0.5D0*dzj
- xj=mod(xj,boxxsize)
- if (xj.lt.0) xj=xj+boxxsize
- yj=mod(yj,boxysize)
- if (yj.lt.0) yj=yj+boxysize
- zj=mod(zj,boxzsize)
- if (zj.lt.0) zj=zj+boxzsize
- if ((zj.lt.0).or.(xj.lt.0).or.(yj.lt.0)) write (*,*) "CHUJ"
- dist_init=(xj-xmedi)**2+(yj-ymedi)**2+(zj-zmedi)**2
- xj_safe=xj
- yj_safe=yj
- zj_safe=zj
- isubchap=0
- do xshift=-1,1
- do yshift=-1,1
- do zshift=-1,1
- xj=xj_safe+xshift*boxxsize
- yj=yj_safe+yshift*boxysize
- zj=zj_safe+zshift*boxzsize
- dist_temp=(xj-xmedi)**2+(yj-ymedi)**2+(zj-zmedi)**2
- if(dist_temp.lt.dist_init) then
- dist_init=dist_temp
- xj_temp=xj
- yj_temp=yj
- zj_temp=zj
- isubchap=1
- endif
- enddo
- enddo
- enddo
- if (isubchap.eq.1) then
- xj=xj_temp-xmedi
- yj=yj_temp-ymedi
- zj=zj_temp-zmedi
- else
- xj=xj_safe-xmedi
- yj=yj_safe-ymedi
- zj=zj_safe-zmedi
- endif
-C if ((i+3).lt.j) then !this condition keeps for turn3 and turn4 not subject to PBC
-c 174 continue
-c if (xj.gt.((0.5d0)*boxxsize)) xj=xj-boxxsize
-c if (xj.lt.((-0.5d0)*boxxsize)) xj=xj+boxxsize
-C Condition for being inside the proper box
-c if ((xj.gt.((0.5d0)*boxxsize)).or.
-c & (xj.lt.((-0.5d0)*boxxsize))) then
-c go to 174
-c endif
-c 175 continue
-c if (yj.gt.((0.5d0)*boxysize)) yj=yj-boxysize
-c if (yj.lt.((-0.5d0)*boxysize)) yj=yj+boxysize
-C Condition for being inside the proper box
-c if ((yj.gt.((0.5d0)*boxysize)).or.
-c & (yj.lt.((-0.5d0)*boxysize))) then
-c go to 175
-c endif
-c 176 continue
-c if (zj.gt.((0.5d0)*boxzsize)) zj=zj-boxzsize
-c if (zj.lt.((-0.5d0)*boxzsize)) zj=zj+boxzsize
-C Condition for being inside the proper box
-c if ((zj.gt.((0.5d0)*boxzsize)).or.
-c & (zj.lt.((-0.5d0)*boxzsize))) then
-c go to 176
-c endif
-C endif !endPBC condintion
-C xj=xj-xmedi
-C yj=yj-ymedi
-C zj=zj-zmedi
+ call to_box(xj,yj,zj)
+ call lipid_layer(xj,yj,zj,sslipj,ssgradlipj)
+ faclipij=(sslipi+sslipj)/2.0d0*lipscale+1.0d0
+ faclipij2=(sslipi+sslipj)/2.0d0*lipscale**2+1.0d0
+ xj=boxshift(xj-xmedi,boxxsize)
+ yj=boxshift(yj-ymedi,boxysize)
+ zj=boxshift(zj-zmedi,boxzsize)
rij=xj*xj+yj*yj+zj*zj
sss=sscale(sqrt(rij))
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
+ ees=ees+eesij*sss*faclipij2
else
fac_shield(i)=1.0
fac_shield(j)=1.0
eesij=(el1+el2)
- ees=ees+eesij
+ ees=ees+eesij*sss*faclipij2
endif
- evdw1=evdw1+evdwij*sss
+ evdw1=evdw1+evdwij*sss*faclipij2
cd write(iout,'(2(2i3,2x),7(1pd12.4)/2(3(1pd12.4),5x)/)')
cd & iteli,i,itelj,j,aaa,bbb,ael6i,ael3i,
cd & 1.0D0/dsqrt(rrmij),evdwij,eesij,
cd & xmedi,ymedi,zmedi,xj,yj,zj
if (energy_dec) then
- write (iout,'(a6,2i5,0pf7.3,2i5,3e11.3)')
- &'evdw1',i,j,evdwij
- &,iteli,itelj,aaa,evdw1,sss
- write (iout,'(a6,2i5,0pf7.3,2f8.3)') 'ees',i,j,eesij,
- &fac_shield(i),fac_shield(j)
+ write (iout,'(a6,2i5,0pf7.3,2i5,3e11.3)')
+ &' evdw1',i,j,evdwij,iteli,itelj,aaa,evdw1,sss
+ write (iout,'(a6,2i5,0pf7.3,6f8.5)') 'ees',i,j,eesij,
+ & fac_shield(i),fac_shield(j),sslipi,sslipj,faclipij,
+ & faclipij2
endif
C
* Radial derivatives. First process both termini of the fragment (i,j)
*
if (calc_grad) then
- ggg(1)=facel*xj
- ggg(2)=facel*yj
- ggg(3)=facel*zj
+ aux=(facel*sss+rmij*sssgrad*eesij)*faclipij2
+ ggg(1)=aux*xj
+ ggg(2)=aux*yj
+ ggg(3)=aux*zj
if ((fac_shield(i).gt.0).and.(fac_shield(j).gt.0).and.
& (shield_mode.gt.0)) then
C print *,i,j
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)
+ gelc_long(3,j)=gelc_long(3,j)+
+ & ssgradlipj*eesij/2.0d0*lipscale**2*sss
+
+ gelc_long(3,i)=gelc_long(3,i)+
+ & ssgradlipi*eesij/2.0d0*lipscale**2*sss
enddo
C print *,"bafter", gelc_long(1,i), gelc_long(1,j)
cgrad enddo
cgrad enddo
if (sss.gt.0.0) then
- facvdw=facvdw+sssgrad*rmij*evdwij
+ facvdw=(facvdw+sssgrad*rmij*evdwij)*faclipij2
ggg(1)=facvdw*xj
ggg(2)=facvdw*yj
ggg(3)=facvdw*zj
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.
*
endif ! calc_grad
#else
C MARYSIA
- facvdw=(ev1+evdwij)
+ facvdw=(ev1+evdwij)*faclipij2
facel=(el1+eesij)
fac1=fac
fac=-3*rrmij*(facvdw+facvdw+facel)*sss
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 ! calc_grad
#endif
*
cd & (dcosg(k),k=1,3)
do k=1,3
ggg(k)=(ecosb*dcosb(k)+ecosg*dcosg(k))*
- & fac_shield(i)**2*fac_shield(j)**2
+ & fac_shield(i)**2*fac_shield(j)**2*sss*faclipij2
enddo
c do k=1,3
c ghalf=0.5D0*ggg(k)
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))
- & *fac_shield(i)**2*fac_shield(j)**2
+ & *fac_shield(i)**2*fac_shield(j)**2*faclipij2
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
+ & *fac_shield(i)**2*fac_shield(j)**2*faclipij2
gelc_long(k,j)=gelc_long(k,j)+ggg(k)
gelc_long(k,i)=gelc_long(k,i)-ggg(k)
enddo
C fac_shield(j)=0.6
endif
eel_loc_ij=eel_loc_ij
- & *fac_shield(i)*fac_shield(j)*sss
+ & *fac_shield(i)*fac_shield(j)*sss*faclipij
if (energy_dec) write (iout,'(a6,2i5,0pf7.3)')
& 'eelloc',i,j,eel_loc_ij
c if (eel_loc_ij.ne.0)
& +a23*gmuij1(2)
& +a32*gmuij1(3)
& +a33*gmuij1(4))
- & *fac_shield(i)*fac_shield(j)*sss
+ & *fac_shield(i)*fac_shield(j)*sss*faclipij
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)*sss
+ & *fac_shield(i)*fac_shield(j)*sss*faclipij
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)
+ & *fac_shield(i)*fac_shield(j)*sss*faclipij
geel_loc_ji=
& +a22*gmuji2(1)
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)*sss
+ & *fac_shield(i)*fac_shield(j)*sss*faclipij
#endif
cd write (iout,*) 'i',i,' j',j,' eel_loc_ij',eel_loc_ij
& 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))
- & *fac_shield(i)*fac_shield(j)
+ & *fac_shield(i)*fac_shield(j)*sss*faclipij
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)
+ & *fac_shield(i)*fac_shield(j)*sss*faclipij
C Derivatives of eello in DC(i+1) thru DC(j-1) or DC(nres-2)
aux=eel_loc_ij/sss*sssgrad*rmij
ggg(1)=aux*xj
do l=1,3
ggg(l)=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)*sss
+ & *fac_shield(i)*fac_shield(j)*sss*faclipij
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/faclipij
+
+ gel_loc_long(3,i)=gel_loc_long(3,i)+
+ & ssgradlipi*eel_loc_ij/2.0d0*lipscale/faclipij
cgrad do k=i+1,j2
cgrad do l=1,3
cgrad gel_loc(l,k)=gel_loc(l,k)+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)
+ & *fac_shield(i)*fac_shield(j)*sss*faclipij
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)
+ & *fac_shield(i)*fac_shield(j)*sss*faclipij
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)
+ & *fac_shield(i)*fac_shield(j)*sss*faclipij
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)
+ & *fac_shield(i)*fac_shield(j)*sss*faclipij
enddo
endif ! calc_grad
common /locel/ a_temp,agg,aggi,aggi1,aggj,aggj1,a22,a23,a32,a33,
& dxi,dyi,dzi,dx_normi,dy_normi,dz_normi,xmedi,ymedi,zmedi,
& num_conti,j1,j2
+ double precision sslipi,sslipj,ssgradlipi,ssgradlipj,faclipij
+ common /lipcalc/ sslipi,sslipj,ssgradlipi,ssgradlipj,faclipij
j=i+2
c write (iout,*) "eturn3",i,j,j1,j2
a_temp(1,1)=a22
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)
+ & *fac_shield(i)*fac_shield(j)*faclipij
eello_t3=0.5d0*(pizda(1,1)+pizda(2,2))
& *fac_shield(i)*fac_shield(j)
if (energy_dec) write (iout,'(6heturn3,2i5,0pf7.3)') i,i+2,
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)
+ & *fac_shield(i)*fac_shield(j)*faclipij
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)
+ & *fac_shield(i)*fac_shield(j)*faclipij
C#endif
C Derivatives in shield mode
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)
+ & *fac_shield(i)*fac_shield(j)*faclipij
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)
+ & *fac_shield(i)*fac_shield(j)*faclipij
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)
+ & *fac_shield(i)*fac_shield(j)*faclipij
a_temp(1,1)=aggi1(l,1)!+agg(l,1)
a_temp(1,2)=aggi1(l,2)!+agg(l,2)
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)
+ & *fac_shield(i)*fac_shield(j)*faclipij
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)
+ & *fac_shield(i)*fac_shield(j)*faclipij
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)
+ & *fac_shield(i)*fac_shield(j)*faclipij
enddo
endif ! calc_grad
common /locel/ a_temp,agg,aggi,aggi1,aggj,aggj1,a22,a23,a32,a33,
& dxi,dyi,dzi,dx_normi,dy_normi,dz_normi,xmedi,ymedi,zmedi,
& num_conti,j1,j2
+ double precision sslipi,sslipj,ssgradlipi,ssgradlipj,faclipij
+ common /lipcalc/ sslipi,sslipj,ssgradlipi,ssgradlipj,faclipij
j=i+3
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
C
C fac_shield(j)=0.4
endif
eello_turn4=eello_turn4-(s1+s2+s3)
- & *fac_shield(i)*fac_shield(j)
+ & *fac_shield(i)*fac_shield(j)*faclipij
eello_t4=-(s1+s2+s3)
& *fac_shield(i)*fac_shield(j)
c write(iout,*)'chujOWO', auxvec(1),b1(1,iti2)
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)
+ & *fac_shield(i)*fac_shield(j)*faclipij
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)
+ & *fac_shield(i)*fac_shield(j)*faclipij
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)
+ & *fac_shield(i)*fac_shield(j)*faclipij
if (calc_grad) then
C Cartesian derivatives
C Derivatives of this turn contributions in DC(i+2)
s3=0.5d0*(pizda(1,1)+pizda(2,2))
ggg(l)=-(s1+s2+s3)
gcorr4_turn(l,i+2)=gcorr4_turn(l,i+2)-(s1+s2+s3)
- & *fac_shield(i)*fac_shield(j)
+ & *fac_shield(i)*fac_shield(j)*faclipij
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)
+ & *fac_shield(i)*fac_shield(j)*faclipij
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)
+ & *fac_shield(i)*fac_shield(j)*faclipij
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)
+ & *fac_shield(i)*fac_shield(j)*faclipij
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)
+ & *fac_shield(i)*fac_shield(j)*faclipij
enddo
endif ! calc_grad
xi=0.5D0*(c(1,i)+c(1,i+1))
yi=0.5D0*(c(2,i)+c(2,i+1))
zi=0.5D0*(c(3,i)+c(3,i+1))
-C Returning the ith atom to box
- 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
+ call to_box(xi,yi,zi)
do iint=1,nscp_gr(i)
do j=iscpstart(i,iint),iscpend(i,iint)
yj=c(2,j)
zj=c(3,j)
C returning the jth atom to box
- xj=mod(xj,boxxsize)
- if (xj.lt.0) xj=xj+boxxsize
- yj=mod(yj,boxysize)
- if (yj.lt.0) yj=yj+boxysize
- zj=mod(zj,boxzsize)
- if (zj.lt.0) zj=zj+boxzsize
- dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
- xj_safe=xj
- yj_safe=yj
- zj_safe=zj
- subchap=0
-C Finding the closest jth atom
- 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
+ call to_box(xj,yj,zj)
+ xj=boxshift(xj-xi,boxxsize)
+ yj=boxshift(yj-yi,boxysize)
+ zj=boxshift(zj-zi,boxzsize)
rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
C sss is scaling function for smoothing the cutoff gradient otherwise
C the gradient would not be continuouse
enddo
c min_odl=minval(distancek)
- do kk=1,constr_homology
- if(l_homo(kk,ii)) then
- min_odl=distancek(kk)
- exit
- endif
- enddo
- do kk=1,constr_homology
- if(l_homo(kk,ii) .and. distancek(kk).lt.min_odl)
+ if (nexl.gt.0) then
+ min_odl=0.0d0
+ else
+ do kk=1,constr_homology
+ if(l_homo(kk,ii)) then
+ min_odl=distancek(kk)
+ exit
+ endif
+ enddo
+ do kk=1,constr_homology
+ if(l_homo(kk,ii) .and. distancek(kk).lt.min_odl)
& min_odl=distancek(kk)
- enddo
+ enddo
+ endif
c write (iout,* )"min_odl",min_odl
#ifdef DEBUG
write (iout,*) "ij dij",i,j,dij
C lipid
C--buflipbot--- lipid ends buffore starts
C--bordlipbot--buffore ends
+c call cartprint
+c write (iout,*) "Eliptransfer peplipran",pepliptran
eliptran=0.0
do i=1,nres
C do i=1,1
if (itype(i).eq.ntyp1) cycle
positi=(mod(c(3,i+nres),boxzsize))
if (positi.le.0) positi=positi+boxzsize
+c write(iout,*) "i",i," positi",positi,bordlipbot,buflipbot,
+c & bordliptop
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)
if (positi.lt.buflipbot) then
fracinbuf=1.0d0-
& ((positi-bordlipbot)/lipbufthick)
+c write (iout,*) "i",i,itype(i)," fracinbuf",fracinbuf
+c write (iout,*) "i",i," liptranene",liptranene(itype(i))
C lipbufthick is thickenes of lipid buffore
sslip=sscalelip(fracinbuf)
+c write (iout,*) "sslip",sslip
ssgradlip=-sscagradlip(fracinbuf)/lipbufthick
eliptran=eliptran+sslip*liptranene(itype(i))
gliptranx(3,i)=gliptranx(3,i)
endif ! if in lipid or buffor
C else
C eliptran=elpitran+0.0 ! I am in water
+c write (iout,*) "eliptran",eliptran
enddo
return
end
projects / unres.git / blobdiff