zj=c(3,nres+j)
call to_box(xj,yj,zj)
call lipid_layer(xj,yj,zj,sslipj,ssgradlipj)
- write (iout,*) "KWA2", itypi,itypj
+! write (iout,*) "KWA2", itypi,itypj
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 &
iabs(itype(jjj,1)).eq.1) then
call ssbond_ene(iii,jjj,eij)
ehpb=ehpb+2*eij
-!d write (iout,*) "eij",eij
+! write (iout,*) "eij",eij,iii,jjj
endif
else if (ii.gt.nres .and. jj.gt.nres) then
!c Restraints from contact prediction
itypj=iabs(itype(j,1))
! dscj_inv=dsc_inv(itypj)
dscj_inv=vbld_inv(nres+j)
- 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)
eij=akcm*deltad*deltad+akth*(deltat1*deltat1+deltat2*deltat2) &
+akct*deltad*deltat12 &
+v1ss*cosphi+v2ss*cosphi*cosphi+v3ss*cosphi*cosphi*cosphi+ebr
-! write(iout,*) i,j,"rij",rij,"d0cm",d0cm," akcm",akcm," akth",akth,
-! & " akct",akct," deltad",deltad," deltat",deltat1,deltat2,
-! & " deltat12",deltat12," eij",eij
+! write(iout,*) i,j,"rij",rij,"d0cm",d0cm," akcm",akcm," akth",akth, &
+! " akct",akct," deltad",deltad," deltat",deltat1,deltat2, &
+! " deltat12",deltat12," eij",eij
ed=2*akcm*deltad+akct*deltat12
pom1=akct*deltad
pom2=v1ss+2*v2ss*cosphi+3*v3ss*cosphi*cosphi
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
real(kind=8) :: facd4, adler, Fgb, facd3
integer troll,jj,istate
real (kind=8) :: dcosom1(3),dcosom2(3)
+ real(kind=8) ::locbox(3)
+ locbox(1)=boxxsize
+ locbox(2)=boxysize
+ locbox(3)=boxzsize
evdw=0.0D0
if (nres_molec(5).eq.0) return
zj=c(3,j)
call to_box(xj,yj,zj)
+! write(iout,*) "xi,yi,zi,xj,yj,zj", xi,yi,zi,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
xj=boxshift(xj-xi,boxxsize)
yj=boxshift(yj-yi,boxysize)
zj=boxshift(zj-zi,boxzsize)
+! write(iout,*) "xj,yj,zj", xj,yj,zj,boxxsize
! dxj = dc_norm( 1, nres+j )
! dyj = dc_norm( 2, nres+j )
ctail(k,1)=c(k,i+nres)
ctail(k,2)=c(k,j)
END DO
+ call to_box(ctail(1,1),ctail(2,1),ctail(3,1))
+ call to_box(ctail(1,2),ctail(2,2),ctail(3,2))
!c! tail distances will be themselves usefull elswhere
!c1 (in Gcav, for example)
- Rtail_distance(1) = ctail( 1, 2 ) - ctail( 1,1 )
- Rtail_distance(2) = ctail( 2, 2 ) - ctail( 2,1 )
- Rtail_distance(3) = ctail( 3, 2 ) - ctail( 3,1 )
+ do k=1,3
+ Rtail_distance(k) = boxshift(ctail(k,2) - ctail(k,1),locbox(k))
+ enddo
Rtail = dsqrt( &
(Rtail_distance(1)*Rtail_distance(1)) &
+ (Rtail_distance(2)*Rtail_distance(2)) &
! see unres publications for very informative images
chead(k,1) = c(k, i+nres) + d1 * dc_norm(k, i+nres)
chead(k,2) = c(k, j)
+ enddo
+ call to_box(chead(1,1),chead(2,1),chead(3,1))
+ call to_box(chead(1,2),chead(2,2),chead(3,2))
+
! distance
! Rsc_distance(k) = dabs(c(k, i+nres) - c(k, j+nres))
-! Rsc(k) = Rsc_distance(k) * Rsc_distance(k)
- Rhead_distance(k) = chead(k,2) - chead(k,1)
+! Rsc(k) = Rsc_distance(k) * Rsc_distance(k)
+ do k=1,3
+ Rhead_distance(k) = boxshift(chead(k,2) - chead(k,1),locbox(k))
END DO
! pitagoras (root of sum of squares)
Rhead = dsqrt( &
dPOLdOM1 = 0.0d0
dPOLdOM2 = 0.0d0
Fcav = 0.0d0
+ Fisocav=0.0d0
dFdR = 0.0d0
dCAVdOM1 = 0.0d0
dCAVdOM2 = 0.0d0
yj=c(2,j)
zj=c(3,j)
call to_box(xj,yj,zj)
+ xj=boxshift(xj-xi,boxxsize)
+ yj=boxshift(yj-yi,boxysize)
+ zj=boxshift(zj-zi,boxzsize)
+
dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
dxj = 0.0d0! dc_norm( 1, nres+j )
ctail(k,1)=(c(k,i)+c(k,i+1))/2.0
ctail(k,2)=c(k,j)
END DO
+ call to_box(ctail(1,1),ctail(2,1),ctail(3,1))
+ call to_box(ctail(1,2),ctail(2,2),ctail(3,2))
+!c! tail distances will be themselves usefull elswhere
+!c1 (in Gcav, for example)
+ do k=1,3
+ Rtail_distance(k) = boxshift(ctail(k,2) - ctail(k,1),locbox(k))
+ enddo
+
!c! tail distances will be themselves usefull elswhere
!c1 (in Gcav, for example)
- Rtail_distance(1) = ctail( 1, 2 ) - ctail( 1,1 )
- Rtail_distance(2) = ctail( 2, 2 ) - ctail( 2,1 )
- Rtail_distance(3) = ctail( 3, 2 ) - ctail( 3,1 )
Rtail = dsqrt( &
(Rtail_distance(1)*Rtail_distance(1)) &
+ (Rtail_distance(2)*Rtail_distance(2)) &
! see unres publications for very informative images
chead(k,1) = (c(k, i)+c(k,i+1))/2.0 + d1 * dc_norm(k, i)
chead(k,2) = c(k, j)
+ ENDDO
! distance
! Rsc_distance(k) = dabs(c(k, i+nres) - c(k, j+nres))
! Rsc(k) = Rsc_distance(k) * Rsc_distance(k)
- Rhead_distance(k) = chead(k,2) - chead(k,1)
+ call to_box(chead(1,1),chead(2,1),chead(3,1))
+ call to_box(chead(1,2),chead(2,2),chead(3,2))
+
+! distance
+! Rsc_distance(k) = dabs(c(k, i+nres) - c(k, j+nres))
+! Rsc(k) = Rsc_distance(k) * Rsc_distance(k)
+ do k=1,3
+ Rhead_distance(k) = boxshift(chead(k,2) - chead(k,1),locbox(k))
END DO
+
! pitagoras (root of sum of squares)
Rhead = dsqrt( &
(Rhead_distance(1)*Rhead_distance(1)) &
yj=c(2,j)
zj=c(3,j)
call to_box(xj,yj,zj)
+! write(iout,*) "xi,yi,zi,xj,yj,zj", xi,yi,zi,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
xj=boxshift(xj-xi,boxxsize)
yj=boxshift(yj-yi,boxysize)
zj=boxshift(zj-zi,boxzsize)
-
+! write(iout,*) 'after shift', xj,yj,zj
dist_init=xj**2+yj**2+zj**2
itypi=itype(i,2)
zi=c(3,nres+i)
call to_box(xi,yi,zi)
call lipid_layer(xi,yi,zi,sslipi,ssgradlipi)
- 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
+! endif
! print *, sslipi,ssgradlipi
dxi=dc_norm(1,nres+i)
dyi=dc_norm(2,nres+i)
zj=c(3,j+nres)
call to_box(xj,yj,zj)
call lipid_layer(xj,yj,zj,sslipj,ssgradlipj)
- write(iout,*) "KRUWA", i,j
+! write(iout,*) "KRUWA", i,j
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 &
projects / unres4.git / blobdiff