Merge branch 'prerelease-3.2.1' into czarek

Conflicts:
	bin/unres/MD-M/unres_Tc_procor_oldparm_em64-D-symetr.exe
	bin/unres/MD/unres_gfortran_single_GAB.exe
	bin/unres/MD/unres_ifort_MPICH_E0LL2Y.exe
	bin/unres/MD/unres_ifort_MPICH_GAB.exe
	examples/unres/new/microcanonical/DYN_SS/hth/small.out_GB000
	examples/unres/new/microcanonical/DYN_SS/hth/small_GB000.stat
	examples/unres/new/microcanonical/DYN_SS/hth/small_MD000.pdb
	source/unres/src_MD/Makefile_MPICH_ifort
	source/unres/src_MD/cinfo.f
	source/unres/src_MD/energy_p_new_barrier.F
	source/unres/src_MD/parmread.F
	source/unres/src_MD/ssMD.F
	source/unres/src_MD/unres.F

diff --cc bin/unres/MD/unres_gfortran_single_GAB.exe
index 56d88f3,fbdcabb..0000000
deleted file mode 100755,100755
Binary files differ

diff --cc bin/unres/MD/unres_ifort_MPICH_GAB.exe
index fed1d51,c021865..97d45b7
Binary files differ

diff --cc examples/unres/new/microcanonical/DYN_SS/hth/small.out_GB000
index 1193edb,5b4bf21..9904891
--- 1/examples/unres/new/microcanonical/DYN_SS/hth/small.out_GB000
--- 2/examples/unres/new/microcanonical/DYN_SS/hth/small.out_GB000
+++ b/examples/unres/new/microcanonical/DYN_SS/hth/small.out_GB000
@@@ -30,8 -30,8 +30,8 @@@ United-residue force field calculation 
  ********************************************************************************
   ### LAST MODIFIED  03/28/12 23:29 by czarek
   ++++ Compile info ++++
-  Version 3.1 build 51
-  compiled Fri Feb 15 09:57:56 2013
 - Version 3.1 build 65
 - compiled Fri Feb 15 13:06:59 2013
++ Version 3.1 build 52
++ compiled Sun Feb 17 00:55:22 2013
   compiled by czarek@piasek3
   OS name:    Linux 
   OS release: 2.6.32-42-generic 
@@@ -39,11 -39,11 +39,11 @@@
   flags:
   INSTALL_DIR = /users/software/mpich-1.2.7p1_int...
   FC= ifort
-- OPT =  -O3 -ip -w 
++ OPT =  -O3 -ip 
   FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include 
-- FFLAGS1 = -c -w -g -d2 -CA -CB -I$(INSTALL_DIR)...
-- FFLAGS2 = -c -w -g -O0 -I$(INSTALL_DIR)/include  
-- FFLAGSE = -c -w -O3 -ipo -ipo_obj  -opt_report ...
++ FFLAGS1 = -c  -g -CA -CB -I$(INSTALL_DIR)/inclu...
++ FFLAGS2 = -c  -g -O0 -I$(INSTALL_DIR)/include  
++ FFLAGSE = -c  -O3 -ipo  -opt_report -I$(INSTALL...
   LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf/libxdr...
   ARCH = LINUX
   PP = /lib/cpp -P
@@@ -415,13 -415,13 +415,13 @@@ Initial
  
  ===================================  Timing  ===================================
  
--                  MD calculations setup:    1.17188E-02
-            Energy & gradient evaluation:    1.82461E+01
++                  MD calculations setup:    7.81250E-03
+            Energy & gradient evaluation:    1.83398E+01
                      Stochastic MD setup:    0.00000E+00
                 Stochastic MD step setup:    0.00000E+00
-                                MD steps:    2.22773E+01
 -                               MD steps:    2.30547E+01
++                               MD steps:    2.24727E+01
  
  
  ============================  End of MD calculation  ===========================
  CG processor   0 is finishing work.
-  Total wall clock time   22.3125000000000       sec
 - Total wall clock time   23.0898437500000       sec
++ Total wall clock time   22.5898437500000       sec

diff --cc examples/unres/new/microcanonical/DYN_SS/hth/small_MD000.pdb
index 0ccab6c,01f2611..3d26e9a
--- 1/examples/unres/new/microcanonical/DYN_SS/hth/small_MD000.pdb
--- 2/examples/unres/new/microcanonical/DYN_SS/hth/small_MD000.pdb
+++ b/examples/unres/new/microcanonical/DYN_SS/hth/small_MD000.pdb
@@@ -5676,9 -5672,8 +5672,8 @@@ CONECT   26   28   2
  CONECT   28   30   29
  CONECT   30   32   31
  CONECT   32   34   33
- CONECT    1    1
  ENDMDL
 -REMARK time  529.65                                       ENERGY    -2.36499E+01
 +REMARK time  529.65                                       ENERGY    -1.81499E+01
  SSBOND   1 CYS    -14    CYS     -5
  ATOM      1  CA  GLY     1      -4.898  -5.564   1.341          0.040
  ATOM      2  CA  ALA     2      -1.912  -4.318  -0.673          0.025
@@@ -5732,9 -5727,8 +5727,8 @@@ CONECT   26   28   2
  CONECT   28   30   29
  CONECT   30   32   31
  CONECT   32   34   33
- CONECT    1    1
  ENDMDL
 -REMARK time  534.65                                       ENERGY    -2.18306E+01
 +REMARK time  534.65                                       ENERGY    -1.63306E+01
  SSBOND   1 CYS    -14    CYS     -5
  ATOM      1  CA  GLY     1      -4.803  -6.813  -0.046          0.062
  ATOM      2  CA  ALA     2      -2.142  -4.422  -1.185          0.025
@@@ -5788,9 -5782,8 +5782,8 @@@ CONECT   26   28   2
  CONECT   28   30   29
  CONECT   30   32   31
  CONECT   32   34   33
- CONECT    1    1
  ENDMDL
 -REMARK time  539.65                                       ENERGY    -2.91310E+01
 +REMARK time  539.65                                       ENERGY    -2.36310E+01
  SSBOND   1 CYS    -14    CYS     -5
  ATOM      1  CA  GLY     1      -4.887  -7.438  -1.507          0.021
  ATOM      2  CA  ALA     2      -2.308  -4.782  -0.843          0.006
@@@ -5844,9 -5837,8 +5837,8 @@@ CONECT   26   28   2
  CONECT   28   30   29
  CONECT   30   32   31
  CONECT   32   34   33
- CONECT    1    1
  ENDMDL
 -REMARK time  544.64                                       ENERGY    -3.10983E+01
 +REMARK time  544.64                                       ENERGY    -2.55983E+01
  SSBOND   1 CYS    -14    CYS     -5
  ATOM      1  CA  GLY     1      -3.390  -6.761  -2.748          0.021
  ATOM      2  CA  ALA     2      -2.839  -4.850   0.536          0.057
@@@ -5900,9 -5892,8 +5892,8 @@@ CONECT   26   28   2
  CONECT   28   30   29
  CONECT   30   32   31
  CONECT   32   34   33
- CONECT    1    1
  ENDMDL
 -REMARK time  549.62                                       ENERGY    -1.85015E+01
 +REMARK time  549.62                                       ENERGY    -1.30015E+01
  SSBOND   1 CYS    -14    CYS     -5
  ATOM      1  CA  GLY     1      -2.079  -5.405  -2.917          0.049
  ATOM      2  CA  ALA     2      -3.379  -4.925   0.632          0.015
@@@ -5956,9 -5947,8 +5947,8 @@@ CONECT   26   28   2
  CONECT   28   30   29
  CONECT   30   32   31
  CONECT   32   34   33
- CONECT    1    1
  ENDMDL
 -REMARK time  554.62                                       ENERGY    -3.01767E+01
 +REMARK time  554.62                                       ENERGY    -2.46767E+01
  SSBOND   1 CYS    -14    CYS     -5
  ATOM      1  CA  GLY     1      -3.630  -4.353  -3.247          0.063
  ATOM      2  CA  ALA     2      -2.835  -4.497   0.440          0.015
@@@ -6012,9 -6002,8 +6002,8 @@@ CONECT   26   28   2
  CONECT   28   30   29
  CONECT   30   32   31
  CONECT   32   34   33
- CONECT    1    1
  ENDMDL
 -REMARK time  559.62                                       ENERGY    -2.63250E+01
 +REMARK time  559.62                                       ENERGY    -2.08250E+01
  SSBOND   1 CYS    -14    CYS     -5
  ATOM      1  CA  GLY     1      -4.855  -3.810  -3.007          0.005
  ATOM      2  CA  ALA     2      -2.482  -4.088  -0.078          0.006
@@@ -6068,9 -6057,8 +6057,8 @@@ CONECT   26   28   2
  CONECT   28   30   29
  CONECT   30   32   31
  CONECT   32   34   33
- CONECT    1    1
  ENDMDL
 -REMARK time  564.57                                       ENERGY    -3.11699E+01
 +REMARK time  564.57                                       ENERGY    -2.56699E+01
  SSBOND   1 CYS    -14    CYS     -5
  ATOM      1  CA  GLY     1      -4.870  -4.554  -2.297          0.028
  ATOM      2  CA  ALA     2      -2.163  -3.024  -0.123          0.003
@@@ -6124,9 -6112,8 +6112,8 @@@ CONECT   26   28   2
  CONECT   28   30   29
  CONECT   30   32   31
  CONECT   32   34   33
- CONECT    1    1
  ENDMDL
 -REMARK time  569.57                                       ENERGY    -3.02057E+01
 +REMARK time  569.57                                       ENERGY    -2.47057E+01
  SSBOND   1 CYS    -14    CYS     -5
  ATOM      1  CA  GLY     1      -4.488  -4.864  -2.047          0.006
  ATOM      2  CA  ALA     2      -2.257  -2.614  -0.060          0.019
@@@ -6830,9 -6816,8 +6816,8 @@@ CONECT   26   28   2
  CONECT   28   30   29
  CONECT   30   32   31
  CONECT   32   34   33
- CONECT    1    1
  ENDMDL
 -REMARK time  634.56                                       ENERGY    -2.12068E+01
 +REMARK time  634.56                                       ENERGY    -1.57068E+01
  SSBOND   1 CYS    -14    CYS     -5
  ATOM      1  CA  GLY     1       0.306   4.023  -1.218          0.043
  ATOM      2  CA  ALA     2       0.718   0.868   0.849          0.038
@@@ -7914,9 -7898,8 +7898,8 @@@ CONECT   26   28   2
  CONECT   28   30   29
  CONECT   30   32   31
  CONECT   32   34   33
- CONECT    1    1
  ENDMDL
 -REMARK time  734.50                                       ENERGY    -3.02457E+01
 +REMARK time  734.50                                       ENERGY    -2.47457E+01
  SSBOND   1 CYS    -14    CYS     -5
  ATOM      1  CA  GLY     1      -0.090  -4.138  -4.253          0.038
  ATOM      2  CA  ALA     2      -1.821  -1.719  -1.900          0.014
@@@ -7970,9 -7953,8 +7953,8 @@@ CONECT   26   28   2
  CONECT   28   30   29
  CONECT   30   32   31
  CONECT   32   34   33
- CONECT    1    1
  ENDMDL
 -REMARK time  739.50                                       ENERGY    -3.37480E+01
 +REMARK time  739.50                                       ENERGY    -2.82480E+01
  SSBOND   1 CYS    -14    CYS     -5
  ATOM      1  CA  GLY     1       0.680  -4.094  -4.317          0.008
  ATOM      2  CA  ALA     2      -1.615  -2.206  -1.889          0.090
@@@ -8026,9 -8008,8 +8008,8 @@@ CONECT   26   28   2
  CONECT   28   30   29
  CONECT   30   32   31
  CONECT   32   34   33
- CONECT    1    1
  ENDMDL
 -REMARK time  744.50                                       ENERGY    -3.42503E+01
 +REMARK time  744.50                                       ENERGY    -2.87503E+01
  SSBOND   1 CYS    -14    CYS     -5
  ATOM      1  CA  GLY     1       1.142  -3.973  -4.298          0.006
  ATOM      2  CA  ALA     2      -1.738  -2.746  -2.214          0.030

diff --cc source/unres/src_MD-M/energy_p_new_barrier.F
Simple merge

diff --cc source/unres/src_MD/cinfo.f
index d2b4e20,4cc77de..3f50f77
--- 1/source/unres/src_MD/cinfo.f
--- 2/source/unres/src_MD/cinfo.f
+++ b/source/unres/src_MD/cinfo.f
@@@ -1,10 -1,10 +1,10 @@@
  C DO NOT EDIT THIS FILE - IT HAS BEEN GENERATED BY COMPINFO.C
- C 3 1 51
 -C 3 1 69
++C 3 1 52
        subroutine cinfo
        include 'COMMON.IOUNITS'
        write(iout,*)'++++ Compile info ++++'
-       write(iout,*)'Version 3.1 build 51'
-       write(iout,*)'compiled Fri Feb 15 09:57:56 2013'
 -      write(iout,*)'Version 3.1 build 69'
 -      write(iout,*)'compiled Sat Feb 16 13:00:53 2013'
++      write(iout,*)'Version 3.1 build 52'
++      write(iout,*)'compiled Sun Feb 17 00:55:22 2013'
        write(iout,*)'compiled by czarek@piasek3'
        write(iout,*)'OS name:    Linux '
        write(iout,*)'OS release: 2.6.32-42-generic '

diff --cc source/unres/src_MD/energy_p_new_barrier.F
Simple merge

diff --cc source/unres/src_MD/geomout.F
Simple merge

diff --cc source/unres/src_MD/initialize_p.F
Simple merge

diff --cc source/unres/src_MD/parmread.F
index cd9bda2,bdc3809..13f4882
--- 1/source/unres/src_MD/parmread.F
--- 2/source/unres/src_MD/parmread.F
+++ b/source/unres/src_MD/parmread.F
@@@ -565,8 -565,7 +565,8 @@@ cc maxinter is maximum interaction site
        do l=1,maxinter    
        do i=1,nsccortyp
        do j=1,nsccortyp
-         read (isccor,*,end=1113,err=1113) 
-      &           nterm_sccor(i,j),nlor_sccor(i,j)
 -        read (isccor,*,end=119,err=119) nterm_sccor(i,j),nlor_sccor(i,j)
++        read (isccor,*,end=119,err=119) 
++     &          nterm_sccor(i,j),nlor_sccor(i,j)
            v0ijsccor=0.0d0
            si=-1.0d0