X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fsrc_MD-M%2Finitialize_p.F;h=da0d3f9019b0ccefe24e576f091b6454a20c823b;hb=e4035e50115ab9c0e65b0445aed96096a5cb86d5;hp=718e60ee9c3a76f40a92cca4029167cc1595d380;hpb=78c6b598700d2c701af6532afb20ebc905a0b8ef;p=unres.git

diff --git a/source/unres/src_MD-M/initialize_p.F b/source/unres/src_MD-M/initialize_p.F
index 718e60e..da0d3f9 100644
--- a/source/unres/src_MD-M/initialize_p.F
+++ b/source/unres/src_MD-M/initialize_p.F
@@ -119,6 +119,14 @@ C
       icsa_in=40
 crc for ifc error 118
       icsa_pdb=42
+C Lipidic input file for parameters range 60-79
+      iliptranpar=60
+C input file for transfer sidechain and peptide group inside the
+C lipidic environment if lipid is implicite
+
+C DNA input files for parameters range 80-99
+C Suger input files for parameters range 100-119
+C All-atom input files for parameters range 120-149
 C
 C Set default weights of the energy terms.
 C
@@ -146,8 +154,10 @@ c      call memmon_print_usage()
       enddo
       do i=1,ntyp
 	do j=1,ntyp
-	  aa(i,j)=0.0D0
-	  bb(i,j)=0.0D0
+	  aa_aq(i,j)=0.0D0
+	  bb_aq(i,j)=0.0D0
+          aa_lip(i,j)=0.0D0
+          bb_lip(i,j)=0.0D0
 	  augm(i,j)=0.0D0
 	  sigma(i,j)=0.0D0
 	  r0(i,j)=0.0D0
@@ -245,6 +255,32 @@ C Initialize the bridge arrays
 	ihpb(i)=0
 	jhpb(i)=0
       enddo
+C Initialize correlation arrays
+      do i=1,maxres
+       do k=1,2
+        b1(k,i)=0.0
+        b2(k,i)=0.0
+        b1tilde(k,i)=0.0
+c        b2tilde(k,i)=0.0
+        do j=1,2
+C        CC(j,k,i)=0.0
+C        Ctilde(j,k,i)=0.0
+C        DD(j,k,i)=0.0
+C        Dtilde(j,k,i)=0.0
+        EE(j,k,i)=0.0
+        enddo
+       enddo
+      enddo
+      do i=-maxtor,maxtor
+       do k=1,2
+        do j=1,2
+        CC(j,k,i)=0.0
+        Ctilde(j,k,i)=0.0
+        DD(j,k,i)=0.0
+        Dtilde(j,k,i)=0.0
+        enddo
+      enddo
+      enddo
 C
 C Initialize timing.
 C
@@ -267,8 +303,8 @@ C
 C Initialize constants used to split the energy into long- and short-range
 C components
 C
-      r_cut=2.0d0
-      rlamb=0.3d0
+C      r_cut=2.0d0
+C      rlamb=0.3d0
 #ifndef SPLITELE
       nprint_ene=nprint_ene-1
 #endif
@@ -344,7 +380,7 @@ C... to deal with by current processor.
         itask_cont_from(i)=fg_rank
         itask_cont_to(i)=fg_rank
       enddo
-      lprint=.false.
+      lprint=energy_dec
       if (lprint)
      &write (iout,*) 'INIT_INT_TABLE nres=',nres,' nnt=',nnt,' nct=',nct
       n_sc_int_tot=(nct-nnt+1)*(nct-nnt)/2-nss
@@ -443,6 +479,7 @@ c            write (iout,*) 'jj=nct'
       iatsc_s=nnt
       iatsc_e=nct-1
 #endif
+      if (iatsc_s.eq.0) iatsc_s=1
 #ifdef MPI
       if (lprint) write (*,*) 'Processor',fg_rank,' CG Group',kolor,
      &   ' absolute rank',myrank,' iatsc_s=',iatsc_s,' iatsc_e=',iatsc_e
@@ -575,6 +612,7 @@ cd        write (iout,*) 'i.gt.nct-iscp'
         endif 
       enddo ! i
 #endif
+      if (iatscp_s.eq.0) iatscp_s=1
       if (lprint) then
         write (iout,'(a)') 'SC-p interaction array:'
         do i=iatscp_s,iatscp_e
@@ -616,6 +654,8 @@ C Partition local interactions
       call int_bounds(nct-nnt,ibondp_start,ibondp_end) 
       ibondp_start=ibondp_start+nnt
       ibondp_end=ibondp_end+nnt
+      call int_bounds(nres,ilip_start,ilip_end)
+      ilip_start=ilip_start
       call int_bounds1(nres-1,ivec_start,ivec_end) 
 c      print *,"Processor",myrank,fg_rank,fg_rank1,
 c     &  " ivec_start",ivec_start," ivec_end",ivec_end
@@ -627,6 +667,13 @@ c     &  " ivec_start",ivec_start," ivec_end",ivec_end
       else
         call int_bounds(ndih_constr,idihconstr_start,idihconstr_end)
       endif
+      if (ntheta_constr.eq.0) then
+        idihconstr_start=1
+        idihconstr_end=0
+      else
+        call int_bounds
+     &  (ntheta_constr,ithetaconstr_start,ithetaconstr_end)
+      endif
 c      nsumgrad=(nres-nnt)*(nres-nnt+1)/2
 c      nlen=nres-nnt+1
       nsumgrad=(nres-nnt)*(nres-nnt+1)/2
@@ -661,7 +708,10 @@ c      nlen=nres-nnt+1
      & ' ivec_start',ivec_start,' ivec_end',ivec_end,
      & ' iset_start',iset_start,' iset_end',iset_end,
      & ' idihconstr_start',idihconstr_start,' idihconstr_end',
-     &   idihconstr_end
+     &   idihconstr_end,
+     & ' ithetaconstr_start',ithetaconstr_start,' ithetaconstr_end',
+     &   ithetaconstr_end
+
        write (*,*) 'Processor:',fg_rank,myrank,' igrad_start',
      &   igrad_start,' igrad_end',igrad_end,' ngrad_start',ngrad_start,
      &   ' ngrad_end',ngrad_end
@@ -1126,6 +1176,8 @@ c        write (iout,*) "MPI_ROTAT2",MPI_ROTAT2
       iphi1_end=nres
       idihconstr_start=1
       idihconstr_end=ndih_constr
+      ithetaconstr_start=1
+      ithetaconstr_end=ntheta_constr
       iphid_start=iphi_start
       iphid_end=iphi_end-1
       itau_start=4
@@ -1133,13 +1185,16 @@ c        write (iout,*) "MPI_ROTAT2",MPI_ROTAT2
       ibond_start=2
       ibond_end=nres-1
       ibondp_start=nnt
-      ibondp_end=nct-1
+C      ibondp_end=nct-1
+      ibondp_end=nct
       ivec_start=1
       ivec_end=nres-1
       iset_start=3
       iset_end=nres+1
       iint_start=2
       iint_end=nres-1
+      ilip_start=1
+      ilip_end=nres
 #endif
       return
       end