dyi=dc_norm(2,nres+i)
dzi=dc_norm(3,nres+i)
dsci_inv=vbld_inv(i+nres)
-
+ xi=c(1,nres+i)
+ yi=c(2,nres+i)
+ zi=c(3,nres+i)
+ xi=mod(xi,boxxsize)
+ if (xi.lt.0) xi=xi+boxxsize
+ yi=mod(yi,boxysize)
+ if (yi.lt.0) yi=yi+boxysize
+ zi=mod(zi,boxzsize)
+ if (zi.lt.0) zi=zi+boxzsize
+C define scaling factor for lipids
+
+C if (positi.le.0) positi=positi+boxzsize
+C print *,i
+C first for peptide groups
+c for each residue check if it is in lipid or lipid water border area
+ if ((zi.gt.bordlipbot)
+ &.and.(zi.lt.bordliptop)) then
+C the energy transfer exist
+ if (zi.lt.buflipbot) then
+C what fraction I am in
+ fracinbuf=1.0d0-
+ & ((positi-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-positi)/lipbufthick)
+ sslipi=sscalelip(fracinbuf)
+ ssgradlipi=sscagradlip(fracinbuf)/lipbufthick
+ else
+ sslipi=1.0d0
+ ssgradlipi=0.0
+ endif
+ else
+ sslipi=0.0d0
+ ssgradlipi=0.0
+ endif
itypj=itype(j)
- xj=c(1,nres+j)-c(1,nres+i)
- yj=c(2,nres+j)-c(2,nres+i)
- zj=c(3,nres+j)-c(3,nres+i)
+ xj=c(1,nres+j)
+ yj=c(2,nres+j)
+ zj=c(3,nres+j)
+ 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-
+ & ((positi-bordlipbot)/lipbufthick)
+C lipbufthick is thickenes of lipid buffore
+ sslipj=sscalelip(fracinbuf)
+ ssgradlipj=-sscagradlip(fracinbuf)/lipbufthick
+ elseif (zi.gt.bufliptop) then
+ fracinbuf=1.0d0-((bordliptop-positi)/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
+
+ dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
+ xj_safe=xj
+ yj_safe=yj
+ zj_safe=zj
+ subchap=0
+ xj_safe=xj
+ yj_safe=yj
+ zj_safe=zj
+ subchap=0
+ do xshift=-1,1
+ do yshift=-1,1
+ do zshift=-1,1
+ xj=xj_safe+xshift*boxxsize
+ yj=yj_safe+yshift*boxysize
+ zj=zj_safe+zshift*boxzsize
+ dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
+ if(dist_temp.lt.dist_init) then
+ dist_init=dist_temp
+ xj_temp=xj
+ yj_temp=yj
+ zj_temp=zj
+ subchap=1
+ endif
+ enddo
+ enddo
+ enddo
+ if (subchap.eq.1) then
+ xj=xj_temp-xi
+ yj=yj_temp-yi
+ zj=zj_temp-zi
+ else
+ xj=xj_safe-xi
+ yj=yj_safe-yi
+ zj=zj_safe-zi
+ endif
+
+C xj=c(1,nres+j)-c(1,nres+i)
+C yj=c(2,nres+j)-c(2,nres+i)
+C zj=c(3,nres+j)-c(3,nres+i)
dxj=dc_norm(1,nres+j)
dyj=dc_norm(2,nres+j)
dzj=dc_norm(3,nres+j)
rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
rij=dsqrt(rrij) ! sc_angular needs rij to really be the inverse
+ sss=sscale((1.0d0/rij)/sigma(itypi,itypj))
+ sssgrad=sscagrad((1.0d0/rij)/sigma(itypi,itypj))
c The following are set in sc_angular
c erij(1)=xj*rij
c erij(2)=yj*rij
ljXs=sig-sig0ij
ljA=eps1*eps2rt**2*eps3rt**2
- ljB=ljA*bb(itypi,itypj)
- ljA=ljA*aa(itypi,itypj)
- ljxm=ljXs+(-2.0D0*aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
+ ljB=ljA*bb
+ ljA=ljA*aa
+ ljxm=ljXs+(-2.0D0*aa/bb)**(1.0D0/6.0D0)
ssXs=d0cm
deltat1=1.0d0-om1
c Stop and plot energy and derivative as a function of distance
if (checkstop) then
ssm=ssC-0.25D0*ssB*ssB/ssA
- ljm=-0.25D0*ljB*bb(itypi,itypj)/aa(itypi,itypj)
+ ljm=-0.25D0*ljB*bb/aa
if (ssm.lt.ljm .and.
& dabs(rij-0.5d0*(ssxm+ljxm)).lt.0.35d0*(ljxm-ssxm)) then
nicheck=1000
havebond=.false.
ljd=rij-ljXs
fac=(1.0D0/ljd)**expon
- e1=fac*fac*aa(itypi,itypj)
- e2=fac*bb(itypi,itypj)
+ e1=fac*fac*aa
+ e2=fac*bb
eij=eps1*eps2rt*eps3rt*(e1+e2)
eps2der=eij*eps3rt
eps3der=eij*eps2rt
- eij=eij*eps2rt*eps3rt
+ eij=eij*eps2rt*eps3rt*sss
sigder=-sig/sigsq
e1=e1*eps1*eps2rt**2*eps3rt**2
ed=-expon*(e1+eij)/ljd
sigder=ed*sigder
+ ed=ed+eij/sss*sssgrad/sigma(itypi,itypj)*rij
eom1=eps2der*eps2rt_om1-2.0D0*alf1*eps3der+sigder*sigsq_om1
eom2=eps2der*eps2rt_om2+2.0D0*alf2*eps3der+sigder*sigsq_om2
eom12=eij*eps1_om12+eps2der*eps2rt_om12
havebond=.true.
ssd=rij-ssXs
eij=ssA*ssd*ssd+ssB*ssd+ssC
-
+ eij=eij*sss
ed=2*akcm*ssd+akct*deltat12
+ ed=ed+eij/sss*sssgrad/sigma(itypi,itypj)*rij
pom1=akct*ssd
pom2=v1ss+2*v2ss*cosphi+3*v3ss*cosphi*cosphi
eom1=-2*akth*deltat1-pom1-om2*pom2
fac1=deltasq_inv*fac*(xm-rij)
fac2=deltasq_inv*fac*(rij-ssxm)
ed=delta_inv*(Ht*hd2-ssm*hd1)
+ eij=eij*sss
+ ed=ed+eij/sss*sssgrad/sigma(itypi,itypj)*rij
eom1=fac1*d_ssxm(1)+fac2*d_xm(1)+h1*d_ssm(1)
eom2=fac1*d_ssxm(2)+fac2*d_xm(2)+h1*d_ssm(2)
eom12=fac1*d_ssxm(3)+fac2*d_xm(3)+h1*d_ssm(3)
else
havebond=.false.
- ljm=-0.25D0*ljB*bb(itypi,itypj)/aa(itypi,itypj)
- d_ljm(1)=-0.5D0*bb(itypi,itypj)/aa(itypi,itypj)*ljB
+ ljm=-0.25D0*ljB*bb/aa
+ d_ljm(1)=-0.5D0*bb/aa*ljB
d_ljm(2)=d_ljm(1)*(0.5D0*eps2rt_om2/eps2rt+alf2/eps3rt)
d_ljm(3)=d_ljm(1)*(0.5D0*eps1_om12+0.5D0*eps2rt_om12/eps2rt-
+ alf12/eps3rt)
fac1=deltasq_inv*fac*(ljxm-rij)
fac2=deltasq_inv*fac*(rij-xm)
ed=delta_inv*(ljm*hd2-Ht*hd1)
+ eij=eij*sss
+ ed=ed+eij/sss*sssgrad/sigma(itypi,itypj)*rij
eom1=fac1*d_xm(1)+fac2*d_ljxm(1)+h2*d_ljm(1)
eom2=fac1*d_xm(2)+fac2*d_ljxm(2)+h2*d_ljm(2)
eom12=fac1*d_xm(3)+fac2*d_ljxm(3)+h2*d_ljm(3)
checkstop=.false.
endif
c-------END TESTING CODE
+ gg_lipi(3)=ssgradlipi*eij
+ gg_lipj(3)=ssgradlipj*eij
do k=1,3
dcosom1(k)=(dc_norm(k,nres+i)-om1*erij(k))/rij
gg(k)=ed*erij(k)+eom1*dcosom1(k)+eom2*dcosom2(k)
enddo
do k=1,3
- gvdwx(k,i)=gvdwx(k,i)-gg(k)
+ gvdwx(k,i)=gvdwx(k,i)-gg(k)+gg_lipi(k)
& +(eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i))
& +eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv
- gvdwx(k,j)=gvdwx(k,j)+gg(k)
+ gvdwx(k,j)=gvdwx(k,j)+gg(k)+gg_lipj(k)
& +(eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,nres+j))
& +eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv
enddo
cgrad enddo
do l=1,3
- gvdwc(l,i)=gvdwc(l,i)-gg(l)
- gvdwc(l,j)=gvdwc(l,j)+gg(l)
+ gvdwc(l,i)=gvdwc(l,i)-gg(l)+gg_lipi(k)
+ gvdwc(l,j)=gvdwc(l,j)+gg(l)+gg_lipj(k)
enddo
return
projects / unres.git / blobdiff