X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fgeometry.F90;h=c89442f3ab68cf4f4efab0bc9a1fa347151bd5a2;hb=a18045ea1a2b2658ffe57821e33d4231012a77cf;hp=510a8e7bf0092f99dcdc9c9799234370cc39bae0;hpb=3ce440c28eb689f7b4f041a0bb0d92321499808a;p=unres4.git

diff --git a/source/unres/geometry.F90 b/source/unres/geometry.F90
index 510a8e7..c89442f 100644
--- a/source/unres/geometry.F90
+++ b/source/unres/geometry.F90
@@ -453,7 +453,7 @@
 !        print *,i,vbld(i),"vbld(i)"
         vbld_inv(i)=1.0d0/vbld(i)
         vbld(nres+i)=dist(nres+i,i)
-        if (itype(i,1).ne.10) then
+        if ((itype(i,1).ne.10).and.(molnum(i).ne.5)) then
           vbld_inv(nres+i)=1.0d0/vbld(nres+i)
         else
           vbld_inv(nres+i)=0.0d0
@@ -1545,6 +1545,7 @@
         dxi=dc_norm(1,nres+i)
         dyi=dc_norm(2,nres+i)
         dzi=dc_norm(3,nres+i)
+        print *,i,itypi,"sc_move"
         dsci_inv=dsc_inv(itypi)
 !
        do iint=1,nint_gr(i)
@@ -1552,6 +1553,8 @@
          if (itype(j,molnum(j)).eq.ntyp1_molec(molnum(j))) cycle
             ind=ind+1
             itypj=iabs(itype(j,molnum(j)))
+        print *,j,itypj,"sc_move"
+
             dscj_inv=dsc_inv(itypj)
             sig0ij=sigma(itypi,itypj)
             chi1=chi(itypi,itypj)
@@ -3364,7 +3367,7 @@
           +gloc(i-1,icg)*dphi(j,2,i+2)+ &
           gloc(i,icg)*dphi(j,1,i+3)+gloc(nres+i-4,icg)*dtheta(j,2,i+1)+ &
           gloc(nres+i-3,icg)*dtheta(j,1,i+2)
-          if(itype(i,1).ne.10) then
+          if((itype(i,1).ne.10).and.(molnum(nres-1).ne.5)) then
            gcart(j,i)=gcart(j,i)+gloc(ialph(i,1),icg)*dalpha(j,2,i)+ &
            gloc(ialph(i,1)+nside,icg)*domega(j,2,i)
           endif
@@ -3382,12 +3385,12 @@
       	   dphi(j,3,nres-1)+gloc(nres-3,icg)*dphi(j,2,nres) &
            +gloc(2*nres-6,icg)* &
            dtheta(j,2,nres-1)+gloc(2*nres-5,icg)*dtheta(j,1,nres)
-          if(itype(nres-2,1).ne.10) then
+          if((itype(nres-2,1).ne.10).and.(molnum(nres-1).ne.5)) then
               gcart(j,nres-2)=gcart(j,nres-2)+gloc(ialph(nres-2,1),icg)* &
      	      dalpha(j,2,nres-2)+gloc(ialph(nres-2,1)+nside,icg)* &
               domega(j,2,nres-2)
           endif
-          if(itype(nres-1,1).ne.10) then
+          if((itype(nres-1,1).ne.10).and.(molnum(nres-1).ne.5)) then
              gcart(j,nres-2)=gcart(j,nres-2)+gloc(ialph(nres-1,1),icg)* &
       	     dalpha(j,1,nres-1)+gloc(ialph(nres-1,1)+nside,icg)* &
              domega(j,1,nres-1)
@@ -3395,7 +3398,7 @@
          enddo
       endif 
 !  Settind dE/ddnres-1       
-!#define DEBUG
+#define DEBUG
 #ifdef DEBUG
           j=1
               write(iout,*)"in int to carta",nres-1,gcart(j,nres-1),gloc(nres-3,icg),dphi(j,3,nres), &
@@ -3414,7 +3417,7 @@
 
 #endif
 !#undef DEBUG
-        if(itype(nres-1,1).ne.10) then
+        if((itype(nres-1,1).ne.10).and.(molnum(nres-1).ne.5)) then
           gcart(j,nres-1)=gcart(j,nres-1)+gloc(ialph(nres-1,1),icg)* &
       	  dalpha(j,2,nres-1)+gloc(ialph(nres-1,1)+nside,icg)* &
           domega(j,2,nres-1)
@@ -3442,7 +3445,7 @@
               write(iout,*)"in int to cart",i, gxcart(j,i),gloc(ialph(i,1),icg),dalpha(j,3,i), &
               gloc(ialph(i,1)+nside,icg),domega(j,3,i)
 #endif
-!#undef DEBUG
+#undef DEBUG
             enddo
          endif	    
        enddo	 	     	  					  		     				 		    	           	
@@ -3556,7 +3559,8 @@
           endif
 !          if (itype(i+1,1).ne.10) then
           if ((itype(i+1,1).ne.10).and.&
-          (itype(i+1,molnum(i+1)).ne.ntyp1_molec(molnum(i+1)))) then
+          (itype(i+1,molnum(i+1)).ne.ntyp1_molec(molnum(i+1))).and.&
+           (molnum(i+1).ne.5)) then
           gxcart(j,i)=gxcart(j,i)-gloc_sc(3,i-1,icg) &
       *dtauangle(j,3,1,i+2)
            gcart(j,i)=gcart(j,i)+gloc_sc(3,i-1,icg) &
@@ -3565,13 +3569,15 @@
           endif
 !          if (itype(i-1,1).ne.10) then
           if ((itype(i-1,1).ne.10).and.&
-          (itype(i-1,molnum(i-1)).ne.ntyp1_molec(molnum(i-1)))) then
+          (itype(i-1,molnum(i-1)).ne.ntyp1_molec(molnum(i-1))).and.&
+         (molnum(i-1).ne.5)) then
            gcart(j,i)=gcart(j,i)+gloc_sc(1,i-2,icg)* &
            dtauangle(j,1,3,i+1)
           endif
 !          if (itype(i+1,1).ne.10) then
           if ((itype(i+1,1).ne.10).and.&
-          (itype(i+1,molnum(i+1)).ne.ntyp1_molec(molnum(i+1)))) then
+          (itype(i+1,molnum(i+1)).ne.ntyp1_molec(molnum(i+1)))&
+       .and. (molnum(i+1).ne.5)) then
            gcart(j,i)=gcart(j,i)+gloc_sc(2,i-1,icg)* &
            dtauangle(j,2,2,i+2)
 !          write(iout,*) "numer",i,gloc_sc(2,i-1,icg),
@@ -4054,8 +4060,11 @@
         do i=1,nres
          if (molnum(i).eq.5) then
           c(1,i)=dmod(c(1,i),boxxsize)
+          if (c(1,i).lt.0) c(1,i)=c(1,i)+boxxsize
           c(2,i)=dmod(c(2,i),boxysize)
+          if (c(2,i).lt.0) c(2,i)=c(2,i)+boxysize
           c(3,i)=dmod(c(3,i),boxzsize)
+          if (c(3,i).lt.0) c(3,i)=c(3,i)+boxzsize
           c(1,i+nres)=dmod(c(1,i+nres),boxxsize)
           c(2,i+nres)=dmod(c(2,i+nres),boxysize)
           c(3,i+nres)=dmod(c(3,i+nres),boxzsize)