Merge branch 'prerelease-3.2.1' of mmka.chem.univ.gda.pl:unres into prerelease-3.2.1

Conflicts:
	source/unres/src_MD/intcartderiv.F

diff --combined bin/unres/MD/unres-mult-symetr_ifort_MPICH_E0LL2Y.exe
index 3128072,3128072..95469a3
Binary files differ

diff --combined bin/unres/MD/unres_ifort_MPICH_E0LL2Y.exe
index 0aff9aa,0aff9aa..8442e63
Binary files differ

diff --combined bin/unres/MINIM/unres_ifort_MIN_single_E0LL2Y.exe
index 23372d3,23372d3..0c0f61c
Binary files differ

diff --combined source/unres/src_CSA/geomout_min.F
index 5dab339,5dab339..5385714
--- 1/source/unres/src_CSA/geomout_min.F
--- 2/source/unres/src_CSA/geomout_min.F
+++ b/source/unres/src_CSA/geomout_min.F
@@@ -23,7 -23,7 +23,7 @@@ cmodel      write (iunit,'(a5,i6)') 'MO
       &           restyp(iti),hfrag(1,j)-1,
       &           restyp(itj),hfrag(2,j)-1,1,hfrag(2,j)-hfrag(1,j)
          else
--             write (iunit,'(a5,i5,1x,a1,i2,1x,a3,i7,2x,a3,i7,i3)') 
++           write (iunit,'(a5,i5,1x,a1,i2,1x,a3,i7,2x,a3,i7,i3,t76,i5)') 
       &           'HELIX',j,'H',j,
       &           restyp(iti),hfrag(1,j)-1,
       &           restyp(itj),hfrag(2,j)-1,1,hfrag(2,j)-hfrag(1,j)

diff --combined source/unres/src_MD-M/DIMENSIONS
index 5131f4e,5131f4e..2b93b81
--- 1/source/unres/src_MD-M/DIMENSIONS
--- 2/source/unres/src_MD-M/DIMENSIONS
+++ b/source/unres/src_MD-M/DIMENSIONS
@@@ -28,7 -28,7 +28,7 @@@ C Max number of symetric chain
        parameter (maxperm=120) 
  C Max. number of variables
        integer maxvar
--      parameter (maxvar=4*maxres)
++      parameter (maxvar=6*maxres)
  C Max. number of groups of interactions that a given SC is involved in
        integer maxint_gr
        parameter (maxint_gr=2)

diff --combined source/unres/src_MD-M/cinfo.f
index db23899,db23899..b3595dd
--- 1/source/unres/src_MD-M/cinfo.f
--- 2/source/unres/src_MD-M/cinfo.f
+++ b/source/unres/src_MD-M/cinfo.f
@@@ -1,31 -1,31 +1,17 @@@
  C DO NOT EDIT THIS FILE - IT HAS BEEN GENERATED BY COMPINFO.C
--<<<<<<< HEAD
--C 0 40360 9
++C 0 40376 2
        subroutine cinfo
        include 'COMMON.IOUNITS'
        write(iout,*)'++++ Compile info ++++'
--      write(iout,*)'Version 0.40360 build 9'
--      write(iout,*)'compiled Fri Jan 23 21:00:08 2015'
--      write(iout,*)'compiled by adam@mmka'
--=======
--C 0 40360 1
--      subroutine cinfo
--      include 'COMMON.IOUNITS'
--      write(iout,*)'++++ Compile info ++++'
--      write(iout,*)'Version 0.40360 build 1'
--      write(iout,*)'compiled Wed Jan  7 10:41:15 2015'
--      write(iout,*)'compiled by czarek@piasek4'
-->>>>>>> 9a082c1ab203120d8e865971546d473fb146fcdc
++      write(iout,*)'Version 0.40376 build 2'
++      write(iout,*)'compiled Sun May 10 03:42:01 2015'
++      write(iout,*)'compiled by adam@piasek4'
        write(iout,*)'OS name:    Linux '
--      write(iout,*)'OS release: 3.2.0-72-generic '
++      write(iout,*)'OS release: 3.2.0-70-generic '
        write(iout,*)'OS version:',
--     & ' #107-Ubuntu SMP Thu Nov 6 14:24:01 UTC 2014 '
++     & ' #105-Ubuntu SMP Wed Sep 24 19:49:16 UTC 2014 '
        write(iout,*)'flags:'
--<<<<<<< HEAD
--      write(iout,*)'INSTALL_DIR = /users/software/mpich-1.2.7p1_int...'
--=======
        write(iout,*)'INSTALL_DIR = /users/software/mpich2-1.4.1p1_in...'
-->>>>>>> 9a082c1ab203120d8e865971546d473fb146fcdc
        write(iout,*)'FC= ifort'
        write(iout,*)'OPT =  -O3 -ip '
        write(iout,*)'FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include '

diff --combined source/unres/src_MD-M/geomout.F
index 51fe4ad,51fe4ad..d21b400
--- 1/source/unres/src_MD-M/geomout.F
--- 2/source/unres/src_MD-M/geomout.F
+++ b/source/unres/src_MD-M/geomout.F
@@@ -24,7 -24,7 +24,7 @@@ cmodel      write (iunit,'(a5,i6)') 'MO
       &           restyp(iti),hfrag(1,j)-1,
       &           restyp(itj),hfrag(2,j)-1,1,hfrag(2,j)-hfrag(1,j)
          else
--             write (iunit,'(a5,i5,1x,a1,i2,1x,a3,i7,2x,a3,i7,i3)') 
++           write (iunit,'(a5,i5,1x,a1,i2,1x,a3,i7,2x,a3,i7,i3,t76,i5)') 
       &           'HELIX',j,'H',j,
       &           restyp(iti),hfrag(1,j)-1,
       &           restyp(itj),hfrag(2,j)-1,1,hfrag(2,j)-hfrag(1,j)

diff --combined source/unres/src_MD/checkder_p.F
index 6f9ca70,fda3a7b..08b7a32
--- 1/source/unres/src_MD/checkder_p.F
--- 2/source/unres/src_MD/checkder_p.F
+++ b/source/unres/src_MD/checkder_p.F
@@@ -284,7 -284,7 +284,7 @@@ C Check the gradient of the energy in C
  c      call intcartderiv
  c      call checkintcartgrad
        call zerograd
-       aincr=1.0D-5
+       aincr=1.0D-6
        write(iout,*) 'Calling CHECK_ECARTINT.'
        nf=0
        icall=0
@@@ -534,13 -534,12 +534,14 @@@ c--------------------------------------
           tauangle(1,i+1)=beta(i-1+nres,i-1,i,i+1)
           omicron(1,i)=alpha(i-2,i-1,i-1+nres)
           omicron(2,i)=alpha(i-1+nres,i-1,i)
+ C        print *,i,omicron(1,i),omicron(2,i)
          endif
          if (itype(i).ne.10) then
           tauangle(2,i+1)=beta(i-2,i-1,i,i+nres)
          endif
          endif
 +c        write (2,*) "i",i,tauangle(1,i+1),tauangle(2,i+1),
 +c     &     omicron(1,i),omicron(2,i)
          omeg(i)=beta(nres+i,i,maxres2,i+1)
          alph(i)=alpha(nres+i,i,maxres2)
          theta(i+1)=alpha(i-1,i,i+1)

diff --combined source/unres/src_MD/cinfo.f
index 788bb9d,aaefbc5..293f867
--- 1/source/unres/src_MD/cinfo.f
--- 2/source/unres/src_MD/cinfo.f
+++ b/source/unres/src_MD/cinfo.f
@@@ -1,37 -1,34 +1,33 @@@
  C DO NOT EDIT THIS FILE - IT HAS BEEN GENERATED BY COMPINFO.C
- C 3 2 161
 -C 3 2 132
++C 3 2 162
        subroutine cinfo
        include 'COMMON.IOUNITS'
        write(iout,*)'++++ Compile info ++++'
-       write(iout,*)'Version 3.2 build 161'
-       write(iout,*)'compiled Thu Mar 26 15:08:13 2015'
-       write(iout,*)'compiled by adam@mmka'
 -      write(iout,*)'Version 3.2 build 132'
 -      write(iout,*)'compiled Mon Jan  5 06:40:38 2015'
++      write(iout,*)'Version 3.2 build 162'
++      write(iout,*)'compiled Sun May 10 03:06:38 2015'
+       write(iout,*)'compiled by adam@piasek4'
        write(iout,*)'OS name:    Linux '
-       write(iout,*)'OS release: 3.2.0-77-generic '
+       write(iout,*)'OS release: 3.2.0-70-generic '
        write(iout,*)'OS version:',
-      & ' #112-Ubuntu SMP Tue Feb 10 15:22:22 UTC 2015 '
+      & ' #105-Ubuntu SMP Wed Sep 24 19:49:16 UTC 2014 '
        write(iout,*)'flags:'
-       write(iout,*)'FC = ifort'
-       write(iout,*)'FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include'
-       write(iout,*)'FFLAGS1 = -c -w -g -d2 -CA -CB -I$(INSTALL_DIR)...'
-       write(iout,*)'FFLAGS2 = -c -w -g -O0 -I$(INSTALL_DIR)/include'
-       write(iout,*)'FFLAGSE = -c -w -O3 -ipo -ipo_obj  -opt_report ...'
-       write(iout,*)'FFLAGS = ${FFLAGS1}'
-       write(iout,*)'FFLAGS2 = ${FFLAGS1}'
-       write(iout,*)'FFLAGSE = ${FFLAGS1}'
-       write(iout,*)'CC = cc'
-       write(iout,*)'CFLAGS = -DLINUX -DPGI -c'
-       write(iout,*)'OPT =  -O3 -ip -w'
-       write(iout,*)'LIBS = -Lxdrf -lxdrf'
 -      write(iout,*)'INSTALL_DIR = /users/software/mpich2-1.0.7'
 -      write(iout,*)'FC= gfortran'
 -      write(iout,*)'OPT =  -O'
 -      write(iout,*)'FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include'
 -      write(iout,*)'FFLAGS1 = -c -I$(INSTALL_DIR)/include'
 -      write(iout,*)'FFLAGS2 = -c -O0 -I$(INSTALL_DIR)/include'
 -      write(iout,*)'FFLAGS3 = -c -O -I$(INSTALL_DIR)/include'
 -      write(iout,*)'FFLAGSE = -c -O3 -I$(INSTALL_DIR)/include'
 -      write(iout,*)'LIBS = -L$(INSTALL_DIR)/lib -lmpich -lpthread x...'
++      write(iout,*)'INSTALL_DIR = /users/software/mpich-1.2.7p1_int...'
++      write(iout,*)'FC= ifort'
++      write(iout,*)'OPT =  -O3 -ip '
++      write(iout,*)'FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include '
++      write(iout,*)'FFLAGS1 = -c  -g -CA -CB -I$(INSTALL_DIR)/inclu...'
++      write(iout,*)'FFLAGS2 = -c  -g -O0 -I$(INSTALL_DIR)/include  '
++      write(iout,*)'FFLAGSE = -c  -O3 -ipo  -opt_report -I$(INSTALL...'
++      write(iout,*)'LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf/libxdr...'
        write(iout,*)'ARCH = LINUX'
        write(iout,*)'PP = /lib/cpp -P'
        write(iout,*)'object = unres.o arcos.o cartprint.o chainbuild...'
 -      write(iout,*)'GAB: CPPFLAGS = -DPROCOR -DLINUX -DG77 -DAMD64 ...'
 -      write(iout,*)'GAB: BIN = ../../../bin/unres/MD/unres_gfort_MP...'
 -      write(iout,*)'4P: CPPFLAGS = -DLINUX -DG77 -DAMD64 -DUNRES -D...'
 -      write(iout,*)'4P: BIN = ../../../bin/unres/MD/unres_gfort_MPI...'
 -      write(iout,*)'E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DG77 -DAMD...'
 -      write(iout,*)'E0LL2Y: BIN = ../../../bin/unres/MD/unres_gfort...'
 +      write(iout,*)'GAB: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DAMD64 ...'
-       write(iout,*)'GAB: BIN = ../../../bin/unres/MD/unres_ifort_si...'
++      write(iout,*)'GAB: BIN = ../../../bin/unres/MD/unres_ifort_MP...'
 +      write(iout,*)'4P: CPPFLAGS = -DLINUX -DPGI -DAMD64 -DUNRES -D...'
-       write(iout,*)'4P: BIN = ../../../bin/unres/MD/unres_ifort_sin...'
++      write(iout,*)'4P: BIN = ../../../bin/unres/MD/unres_ifort_MPI...'
 +      write(iout,*)'E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DAMD...'
 +      write(iout,*)'E0LL2Y: BIN = ../../../bin/unres/MD/unres_ifort...'
        write(iout,*)'++++ End of compile info ++++'
        return
        end

diff --combined source/unres/src_MD/energy_p_new_barrier.F
index 5ae5a43,945c363..47583a4
--- 1/source/unres/src_MD/energy_p_new_barrier.F
--- 2/source/unres/src_MD/energy_p_new_barrier.F
+++ b/source/unres/src_MD/energy_p_new_barrier.F
@@@ -3023,6 -3023,9 +3023,9 @@@
  C Loop over i,i+2 and i,i+3 pairs of the peptide groups
  C
        do i=iturn3_start,iturn3_end
+ C        if (itype(i).eq.21 .or. itype(i+1).eq.21
+ C     &  .or. itype(i+2).eq.21 .or. itype(i+3).eq.21.or.itype(i+4).eq.21)
+ C     &  cycle
          dxi=dc(1,i)
          dyi=dc(2,i)
          dzi=dc(3,i)
@@@ -3038,6 -3041,10 +3041,10 @@@
          num_cont_hb(i)=num_conti
        enddo
        do i=iturn4_start,iturn4_end
+ C        if (itype(i).eq.21 .or. itype(i+1).eq.21
+ C     &  .or. itype(i+2).eq.21 .or. itype(i+3).eq.21.or.itype(i+4).eq.21
+ C     &  .or. itype(i+5).eq.21)
+ C     & cycle
          dxi=dc(1,i)
          dyi=dc(2,i)
          dzi=dc(3,i)
@@@ -3056,6 -3063,8 +3063,8 @@@
  c Loop over all pairs of interacting peptide groups except i,i+2 and i,i+3
  c
        do i=iatel_s,iatel_e
+ C          if (itype(i).eq.21 .or. itype(i+1).eq.21
+ C     &.or.itype(i+2)) cycle
          dxi=dc(1,i)
          dyi=dc(2,i)
          dzi=dc(3,i)
@@@ -3068,6 -3077,8 +3077,8 @@@
  c        write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i)
          num_conti=num_cont_hb(i)
          do j=ielstart(i),ielend(i)
+ C          if (itype(j).eq.21 .or. itype(j+1).eq.21
+ C     &.or.itype(j+2)) cycle
            call eelecij(i,j,ees,evdw1,eel_loc)
          enddo ! j
          num_cont_hb(i)=num_conti
@@@ -4775,7 -4786,7 +4786,7 @@@
       & cosph1(maxsingle),sinph1(maxsingle),cosph2(maxsingle),
       & sinph2(maxsingle),cosph1ph2(maxdouble,maxdouble),
       & sinph1ph2(maxdouble,maxdouble)
-       logical lprn /.false./, lprn1 /.true./
+       logical lprn /.false./, lprn1 /.false./
        etheta=0.0D0
        do i=ithet_start,ithet_end
          if ((itype(i-1).eq.ntyp1).or.(itype(i-2).eq.ntyp1).or.
@@@ -4789,7 -4800,8 +4800,8 @@@
            coskt(k)=dcos(k*theti2)
            sinkt(k)=dsin(k*theti2)
          enddo
-         if (i.gt.3) then
+ C        if (i.gt.3) then
+          if (i.gt.3 .and. itype(i-3).ne.ntyp1) then
  #ifdef OSF
            phii=phi(i)
            if (phii.ne.phii) phii=150.0
@@@ -4803,13 -4815,13 +4815,13 @@@
            enddo
          else
            phii=0.0d0
-           ityp1=nthetyp+1
+           ityp1=ithetyp(itype(i-2))
            do k=1,nsingle
              cosph1(k)=0.0d0
              sinph1(k)=0.0d0
            enddo 
          endif
-         if (i.lt.nres) then
+         if ((i.lt.nres).and. itype(i+1).ne.ntyp1) then
  #ifdef OSF
            phii1=phi(i+1)
            if (phii1.ne.phii1) phii1=150.0
@@@ -4824,7 -4836,7 +4836,7 @@@
            enddo
          else
            phii1=0.0d0
-           ityp3=nthetyp+1
+           ityp3=ithetyp(itype(i))
            do k=1,nsingle
              cosph2(k)=0.0d0
              sinph2(k)=0.0d0
@@@ -4930,11 -4942,11 +4942,9 @@@
            enddo
          enddo
  10      continue
          if (lprn1) write (iout,'(a4,i2,3f8.1,9h ethetai ,f10.5)') 
       &  'ebe', i,theta(i)*rad2deg,phii*rad2deg,
       &   phii1*rad2deg,ethetai
--c        lprn1=.false.
          etheta=etheta+ethetai
          if (i.gt.3) gloc(i-3,icg)=gloc(i-3,icg)+wang*dephii
          if (i.lt.nres) gloc(i-2,icg)=gloc(i-2,icg)+wang*dephii1
@@@ -5958,20 -5970,21 +5968,22 @@@ c      lprn=.true
  c      write (iout,*) "EBACK_SC_COR",iphi_start,iphi_end,nterm_sccor
        esccor=0.0D0
        do i=itau_start,itau_end
+ C        do i=42,42
          esccor_ii=0.0D0
          if ((itype(i-2).eq.ntyp1).or.(itype(i-1).eq.ntyp1)) cycle
          isccori=isccortyp(itype(i-2))
          isccori1=isccortyp(itype(i-1))
          phii=phi(i)
+ 
  cccc  Added 9 May 2012
  cc Tauangle is torsional engle depending on the value of first digit 
  c(see comment below)
  cc Omicron is flat angle depending on the value of first digit 
  c(see comment below)
- 
+ C        print *,i,tauangle(1,i)
          
 -        do intertyp=1,3 !intertyp
 +c        do intertyp=1,3 !intertyp
 +        do intertyp=2,2 !intertyp
  cc Added 09 May 2012 (Adasko)
  cc  Intertyp means interaction type of backbone mainchain correlation: 
  c   1 = SC...Ca...Ca...Ca
@@@ -5996,6 -6009,7 +6008,7 @@@ c   3 = SC...Ca...Ca...SC
            esccor=esccor+v1ij*cosphi+v2ij*sinphi
            gloci=gloci+j*(v2ij*cosphi-v1ij*sinphi)
          enddo
+ C        print *,i,tauangle(1,i),gloci
          gloc_sc(intertyp,i-3,icg)=gloc_sc(intertyp,i-3,icg)+wsccor*gloci
  c        write (iout,*) "WTF",intertyp,i,itype(i),v1ij*cosphi+v2ij*sinphi
  c     &gloc_sc(intertyp,i-3,icg)
@@@ -6008,8 -6022,7 +6021,8 @@@
         enddo !intertyp
        enddo
  c        do i=1,nres
 -c        write (iout,*) "W@T@F",  gloc_sc(1,i,icg),gloc(i,icg)
 +c        write (iout,*) "W@T@F",  gloc_sc(1,i,icg),gloc_sc(2,i,icg),
 +c     &   gloc_sc(3,i,icg)
  c        enddo
        return
        end

diff --combined source/unres/src_MD/geomout.F
index df698f5,df698f5..81f8db4
--- 1/source/unres/src_MD/geomout.F
--- 2/source/unres/src_MD/geomout.F
+++ b/source/unres/src_MD/geomout.F
@@@ -23,7 -23,7 +23,7 @@@ cmodel      write (iunit,'(a5,i6)') 'MO
       &           restyp(iti),hfrag(1,j)-1,
       &           restyp(itj),hfrag(2,j)-1,1,hfrag(2,j)-hfrag(1,j)
          else
--             write (iunit,'(a5,i5,1x,a1,i2,1x,a3,i7,2x,a3,i7,i3)') 
++           write (iunit,'(a5,i5,1x,a1,i2,1x,a3,i7,2x,a3,i7,i3,t76,i5)')
       &           'HELIX',j,'H',j,
       &           restyp(iti),hfrag(1,j)-1,
       &           restyp(itj),hfrag(2,j)-1,1,hfrag(2,j)-hfrag(1,j)

diff --combined source/unres/src_MIN/DIMENSIONS
index 8f3f01c,8f4e5ae..893b9b5
--- 1/source/unres/src_MIN/DIMENSIONS
--- 2/source/unres/src_MIN/DIMENSIONS
+++ b/source/unres/src_MIN/DIMENSIONS
@@@ -16,7 -16,7 +16,7 @@@ C Max. number of coarse-grain processor
        parameter (max_cg_procs=maxprocs)
  C Max. number of AA residues
        integer maxres
--      parameter (maxres=100)
++      parameter (maxres=800)
  C Appr. max. number of interaction sites
        integer maxres2,maxres6,mmaxres2
        parameter (maxres2=2*maxres,maxres6=6*maxres)
@@@ -54,7 -54,7 +54,7 @@@ C virtual-bond angle bending potential
       & mmaxtheterm=maxtheterm)
  c Max number of torsional terms in SCCOR
        integer maxterm_sccor
-       parameter (maxterm_sccor=3)
+       parameter (maxterm_sccor=6)
  C Max. number of lobes in SC distribution
        integer maxlob
        parameter (maxlob=4)

diff --combined source/unres/src_MIN/geomout_min.F
index 5dab339,5dab339..5385714
--- 1/source/unres/src_MIN/geomout_min.F
--- 2/source/unres/src_MIN/geomout_min.F
+++ b/source/unres/src_MIN/geomout_min.F
@@@ -23,7 -23,7 +23,7 @@@ cmodel      write (iunit,'(a5,i6)') 'MO
       &           restyp(iti),hfrag(1,j)-1,
       &           restyp(itj),hfrag(2,j)-1,1,hfrag(2,j)-hfrag(1,j)
          else
--             write (iunit,'(a5,i5,1x,a1,i2,1x,a3,i7,2x,a3,i7,i3)') 
++           write (iunit,'(a5,i5,1x,a1,i2,1x,a3,i7,2x,a3,i7,i3,t76,i5)') 
       &           'HELIX',j,'H',j,
       &           restyp(iti),hfrag(1,j)-1,
       &           restyp(itj),hfrag(2,j)-1,1,hfrag(2,j)-hfrag(1,j)

diff --combined source/unres/src_MIN/unres_min.F
index 3cdbeef,3cdbeef..f1a33c8
--- 1/source/unres/src_MIN/unres_min.F
--- 2/source/unres/src_MIN/unres_min.F
+++ b/source/unres/src_MIN/unres_min.F
@@@ -78,7 -78,7 +78,8 @@@ C Fine-grain slaves just do energy and 
        else if (modecalc.eq.5) then
           call exec_checkgrad
        else
--        write (iout,'(a)') 'This calculation type is not supported',
++        write (iout,'(a,i5)') 
++     &   'This calculation type is not supported',
       &   ModeCalc
        endif
  #ifdef MPI