8/11/12 by Adam: fixed disulfide bridge problems

[unres.git] / source / unres / src_MD / geomout.F

diff --git a/source/unres/src_MD/geomout.F b/source/unres/src_MD/geomout.F
index 460b7be..0a46b14 100644 (file)
--- a/source/unres/src_MD/geomout.F
+++ b/source/unres/src_MD/geomout.F
@@ -79,9 +79,15 @@ cmodel      write (iunit,'(a5,i6)') 'MODEL',1
 
       if (nss.gt.0) then
         do i=1,nss
+         if (dyn_ss) then
           write(iunit,'(a6,i4,1x,a3,i7,4x,a3,i7)') 
-     &         'SSBOND',i,'CYS',ihpb(i)-1-nres,
-     &                    'CYS',jhpb(i)-1-nres
+     &         'SSBOND',i,'CYS',idssb(i)-nnt+1,
+     &                    'CYS',jdssb(i)-nnt+1
+         else
+          write(iunit,'(a6,i4,1x,a3,i7,4x,a3,i7)') 
+     &         'SSBOND',i,'CYS',ihpb(i)-nnt+1-nres,
+     &                    'CYS',jhpb(i)-nnt+1-nres
+         endif
         enddo
       endif
       
@@ -110,7 +116,11 @@ cmodel      write (iunit,'(a5,i6)') 'MODEL',1
         write (iunit,30) ica(nct),ica(nct)+1
       endif
       do i=1,nss
+       if (dyn_ss) then
+        write (iunit,30) ica(idssb(i))+1,ica(jdssb(i))+1
+       else
         write (iunit,30) ica(ihpb(i)-nres)+1,ica(jhpb(i)-nres)+1
+       endif
       enddo
       write (iunit,'(a6)') 'ENDMDL'     
   10  FORMAT ('ATOM',I7,'  CA  ',A3,I6,4X,3F8.3,f15.3)
@@ -406,16 +416,30 @@ c-----------------------------------------------------------------
 #endif
        if (refstr) then
          call rms_nac_nnc(rms,frac,frac_nn,co,.false.)
+        if(tnp .or. tnp1 .or. tnh) then
+        write (line1,'(i10,f15.2,3f12.3,f12.6,f7.2,4f6.3,3f12.3,i5,$)')
+     &          itime,totT,EK,potE,totE,hhh,
+     &          rms,frac,frac_nn,co,amax,kinetic_T,t_bath,gyrate(),me
+          format1="a145"
+        else
           write (line1,'(i10,f15.2,3f12.3,f7.2,4f6.3,3f12.3,i5,$)')
      &          itime,totT,EK,potE,totE,
      &          rms,frac,frac_nn,co,amax,kinetic_T,t_bath,gyrate(),me
           format1="a133"
+        endif
+       else
+        if(tnp .or. tnp1 .or. tnh) then
+          write (line1,'(i10,f15.2,7f12.3,f12.6,i5,$)')
+     &           itime,totT,EK,potE,totE,hhh,
+     &           amax,kinetic_T,t_bath,gyrate(),me
+          format1="a126"
         else
           write (line1,'(i10,f15.2,7f12.3,i5,$)')
      &           itime,totT,EK,potE,totE,
      &           amax,kinetic_T,t_bath,gyrate(),me
           format1="a114"
         endif
+       endif
         if(usampl.and.totT.gt.eq_time) then
            write(line2,'(i5,2f9.4,300f7.4)') iset,uconst,uconst_back,
      &      (qfrag(ii1),ii1=1,nfrag),(qpair(ii2),ii2=1,npair),
@@ -430,6 +454,12 @@ c-----------------------------------------------------------------
            line2=' '
         endif
         if (print_compon) then
+          if(itime.eq.0) then
+           write(format,'(a1,a4,a1,a4,a10)') "(",format1,",",format2,
+     &                                                     ",20a12)"
+           write (istat,format) "#","",
+     &      (ename(print_order(i)),i=1,nprint_ene)
+          endif
           write(format,'(a1,a4,a1,a4,a10)') "(",format1,",",format2,
      &                                                     ",20f12.3)"
           write (istat,format) line1,line2,