Correction of D-AA to parmread

[unres.git] / source / unres / src_MD-M / energy_p_new_barrier.F

diff --git a/source/unres/src_MD-M/energy_p_new_barrier.F b/source/unres/src_MD-M/energy_p_new_barrier.F
index 91a7c94..a20ec7b 100644 (file)
--- a/source/unres/src_MD-M/energy_p_new_barrier.F
+++ b/source/unres/src_MD-M/energy_p_new_barrier.F
@@ -6329,6 +6329,9 @@ 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
@@ -6662,6 +6665,7 @@ C
       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)
@@ -12337,10 +12341,31 @@ 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)
 
@@ -12359,14 +12384,61 @@ C calculte rdiffrence between r and r0
       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
+     &       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
 
@@ -12375,6 +12447,11 @@ C now direction of gg_tube vector
         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)
 C        print *,gg_tube(1,0),"TU"