X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Fwham%2Fsrc-M%2FssMD.F;h=bbf3206e193e9270835de31e8f312e0655c9bbf5;hb=d49e46757e9d141bbeff7e406cbc839fe6ab3952;hp=5080b18de4af0d397add71f44b0b7e753c8c1d33;hpb=c757fb796944088d1e00e131f1c2f9591d1deeda;p=unres.git

diff --git a/source/wham/src-M/ssMD.F b/source/wham/src-M/ssMD.F
index 5080b18..bbf3206 100644
--- a/source/wham/src-M/ssMD.F
+++ b/source/wham/src-M/ssMD.F
@@ -150,11 +150,113 @@ c-------END TESTING CODE
       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)
+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
+            xj=c(1,nres+j)
+            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
 
       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)
+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
+
+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)
@@ -187,9 +289,9 @@ c      om12=dxi*dxj+dyi*dyj+dzi*dzj
 
       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
@@ -223,7 +325,7 @@ c-------TESTING CODE
 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
@@ -248,8 +350,8 @@ c-------END TESTING CODE
         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)
 C        write(iout,*) eij,'TU?1'
         eps2der=eij*eps3rt
@@ -316,8 +418,8 @@ C         write(iout,*) eij,'TU?3'
           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)