5/29/2012 by Adam

1. Fixed NaNs in wham (more stable computation of window free energies).
2. Minor fixes in cluster
3. Added exmaple with minimization in MD examples

diff --git a/bin/unres/MD/unres_ifort_MPICH_E0LL2Y.exe b/bin/unres/MD/unres_ifort_MPICH_E0LL2Y.exe
index 70fd7a9..7e3eb18 100755 (executable)
Binary files a/bin/unres/MD/unres_ifort_MPICH_E0LL2Y.exe and b/bin/unres/MD/unres_ifort_MPICH_E0LL2Y.exe differ

diff --git a/bin/wham/wham_ifort_MPICH_E0LL2Y.exe b/bin/wham/wham_ifort_MPICH_E0LL2Y.exe
index 90bd886..508b4f6 100755 (executable)
Binary files a/bin/wham/wham_ifort_MPICH_E0LL2Y.exe and b/bin/wham/wham_ifort_MPICH_E0LL2Y.exe differ

diff --git a/bin/wham/wham_ifort_MPICH_GAB.exe b/bin/wham/wham_ifort_MPICH_GAB.exe
index 4ac1bc2..3b52754 100755 (executable)
Binary files a/bin/wham/wham_ifort_MPICH_GAB.exe and b/bin/wham/wham_ifort_MPICH_GAB.exe differ

diff --git a/examples/unres/MD/ff_gab/1L2Y_minim.inp b/examples/unres/MD/ff_gab/1L2Y_minim.inp
index 286b667..2830886 100644 (file)
--- a/examples/unres/MD/ff_gab/1L2Y_minim.inp
+++ b/examples/unres/MD/ff_gab/1L2Y_minim.inp
@@ -1,6 +1,6 @@
 1L2Y
 1L2Y

-SEED=-3059743 PDBREF MINIMIZE
-maxmin=1000
+SEED=-3059743 REFSTR PDBREF MINIMIZE
+

 WLONG=1.35279 WSCP=1.59304 WELEC=0.71534 WBOND=1.00000 WANG=1.13873            &
 WSCLOC=0.16258 WTOR=1.98599 WTORD=1.57069 WCORRH=0.42887 WCORR5=0.00000        &
 WCORR6=0.00000 WEL_LOC=0.16036 WTURN3=1.68722 WTURN4=0.66230 WTURN6=0.00000    &
 WLONG=1.35279 WSCP=1.59304 WELEC=0.71534 WBOND=1.00000 WANG=1.13873            &
 WSCLOC=0.16258 WTOR=1.98599 WTORD=1.57069 WCORRH=0.42887 WCORR5=0.00000        &
 WCORR6=0.00000 WEL_LOC=0.16036 WTURN3=1.68722 WTURN4=0.66230 WTURN6=0.00000    &

diff --git a/examples/unres/MD/ff_gab/1L2Y_minim.intin b/examples/unres/MD/ff_gab/1L2Y_minim.intin
new file mode 100644 (file)
index 0000000..e69de29

diff --git a/examples/unres/MD/ff_gab/1L2Y_minim.out_GB b/examples/unres/MD/ff_gab/1L2Y_minim.out_GB
new file mode 100644 (file)
index 0000000..18ee121
--- /dev/null
+++ b/examples/unres/MD/ff_gab/1L2Y_minim.out_GB
@@ -0,0 +1,471 @@
+--------------------------------------------------------------------------------
+                              FILE ASSIGNMENT
+--------------------------------------------------------------------------------
+ Input file                      : 1L2Y_minim.inp
+ Output file                     : 1L2Y_minim.out_GB
+ 
+ Sidechain potential file        : 
+ ../../../../PARAM/sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16-10-8k
+ SCp potential file              : ../../../../PARAM/scp.parm
+ Electrostatic potential file    : ../../../../PARAM/electr_631Gdp.parm
+ Cumulant coefficient file       : 
+ ../../../../PARAM/fourier_opt.parm.1igd_hc_iter3_3
+ Torsional parameter file        : ../../../../PARAM/torsion_631Gdp.parm
+ Double torsional parameter file : ../../../../PARAM/torsion_double_631Gdp.parm
+ SCCOR parameter file : ../../../../PARAM/rotcorr_AM1.parm
+ Bond & inertia constant file    : ../../../../PARAM/bond.parm
+ Bending parameter file          : ../../../../PARAM/thetaml.5parm
+ Rotamer parameter file          : ../../../../PARAM/scgauss.parm
+ Threading database              : ../../../../PARAM/patterns.cart
+--------------------------------------------------------------------------------
+ ### LAST MODIFIED  03/28/12 23:29 by czarek
+ ++++ Compile info ++++
+ Version 2.5 build 34
+ compiled Mon Apr  2 08:16:44 2012
+ compiled by adam@matrix.chem.cornell.edu
+ OS name:    Linux 
+ OS release: 2.6.34.9-69.fc13.x86_64 
+ OS version: #1 SMP Tue May 3 09:23:03 UTC 2011 
+ flags:
+ FC = ifort
+ 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 ...
+ CC = cc
+ CFLAGS = -DLINUX -DPGI -c
+ OPT =  -O3 -ip -w
+ LIBS = -Lxdrf -lxdrf
+ ARCH = LINUX
+ PP = /lib/cpp -P
+ object = unres.o arcos.o cartprint.o chainbuild...
+ GAB: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNRES ...
+ GAB: BIN = ../../../bin/unres/MD/unres_ifort_si...
+ E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNR...
+ E0LL2Y: BIN = ../../../bin/unres/MD/unres_ifort...
+ ++++ End of compile info ++++
+
+Potential is GB , exponents are   6 12
+
+Disulfide bridge parameters:
+S-S bridge energy:      -5.50
+d0cm:      3.78 akcm:     15.10
+akth:     11.00 akct:     12.00
+v1ss:     -1.08 v2ss:      7.61 v3ss:     13.70
+ ran_num  0.930227314089531     
+RMSDBC =        3.0
+RMSDBC1 =        0.5
+RMSDBC1MAX =        1.5
+DRMS    =        0.1
+RMSDBCM =        3.0
+Time limit (min):     960.0
+ RESCALE_MODE           1
+Library  routine used to diagonalize matrices.
+
+********************************************************************************
+                    Options in energy minimization:
+********************************************************************************
+MaxMin: 2000 MaxFun: 5000MinMin: 2000 MinFun: 2000 TolF:   1.00000E-02 RTolF:   1.00000E-04
+
+Energy-term weights (unscaled):
+
+WSCC=     1.352790 (SC-SC)
+WSCP=     1.593040 (SC-p)
+WELEC=    0.715340 (p-p electr)
+WVDWPP=   0.113710 (p-p VDW)
+WBOND=    1.000000 (stretching)
+WANG=     1.138730 (bending)
+WSCLOC=   0.162580 (SC local)
+WTOR=     1.985990 (torsional)
+WTORD=    1.570690 (double torsional)
+WSTRAIN=  1.000000 (SS bridges & dist. cnstr.)
+WEL_LOC=  0.160360 (multi-body 3-rd order)
+WCORR4=   0.428870 (multi-body 4th order)
+WCORR5=   0.000000 (multi-body 5th order)
+WCORR6=   0.000000 (multi-body 6th order)
+WSCCOR=   0.000000 (back-scloc correlation)
+WTURN3=   1.687220 (turns, 3rd order)
+WTURN4=   0.662300 (turns, 4th order)
+WTURN6=   0.000000 (turns, 6th order)
+
+Hydrogen-bonding correlation between contact pairs of peptide groups
+
+Scaling factor of 1,4 SC-p interactions:   0.400
+General scaling factor of SC-p interactions:   1.000
+
+Energy-term weights (scaled):
+
+WSCC=     1.352790 (SC-SC)
+WSCP=     1.593040 (SC-p)
+WELEC=    0.715340 (p-p electr)
+WVDWPP=   0.113710 (p-p VDW)
+WBOND=    1.000000 (stretching)
+WANG=     1.138730 (bending)
+WSCLOC=   0.162580 (SC local)
+WTOR=     1.985990 (torsional)
+WTORD=    1.570690 (double torsional)
+WSTRAIN=  1.000000 (SS bridges & dist. cnstr.)
+WEL_LOC=  0.160360 (multi-body 3-rd order)
+WCORR4=   0.428870 (multi-body 4th order)
+WCORR5=   0.000000 (multi-body 5th order)
+WCORR6=   0.000000 (multi-body 6th order)
+WSCCOR=   0.000000 (back-scloc correlatkion)
+WTURN3=   1.687220 (turns, 3rd order)
+WTURN4=   0.662300 (turns, 4th order)
+WTURN6=   0.000000 (turns, 6th order)
+ Reference temperature for weights calculation:   300.000000000000     
+ Parameters of the SS-bond potential:
+ D0CM   3.78000000000000       AKCM   15.1000000000000       AKTH
+   11.0000000000000       AKCT   12.0000000000000     
+ V1SS  -1.08000000000000       V2SS   7.61000000000000       V3SS
+   13.7000000000000     
+ EBR  -5.50000000000000     
+PDB data will be read from file 1L2Y.pdb
+ Nres:    21
+Backbone and SC coordinates as read from the PDB
+  1 21  D    -9.841   4.399  -5.051       -9.841   4.399  -5.051
+  2 14  ASN  -8.608   3.135  -1.618      -10.407   3.153  -2.437
+  3  5  LEU  -4.923   4.002  -2.452       -4.618   6.091  -1.850
+  4  8  TYR  -3.690   2.738   0.981       -1.959   3.143   3.797
+  5  4  ILE  -5.857  -0.449   0.613       -7.484  -0.369   1.074
+  6 13  GLN  -4.122  -1.167  -2.743       -5.089  -1.450  -4.853
+  7  7  TRP  -0.716  -0.631  -0.993        1.727   0.440   1.450
+  8  5  LEU  -1.641  -2.932   1.963       -2.244  -2.097   3.799
+  9 19  LYS  -3.024  -5.791  -0.269       -3.820  -5.527  -3.146
+ 10 16  ASP   0.466  -6.016  -1.905        0.653  -5.125  -3.676
+ 11 10  GLY   2.060  -6.618   1.593        2.060  -6.618   1.593
+ 12 10  GLY   2.626  -2.967   2.723        2.626  -2.967   2.723
+ 13 20  PRO   6.333  -2.533   3.806        5.724  -2.372   5.058
+ 14 12  SER   7.049  -6.179   2.704        6.757  -6.938   3.675
+ 15 12  SER   6.389  -5.315  -1.015        5.245  -5.350  -1.546
+ 16 10  GLY   9.451  -3.116  -1.870        9.451  -3.116  -1.870
+ 17 18  ARG   7.289   0.084  -2.054        5.225  -1.826  -3.986
+ 18 20  PRO   6.782   3.088   0.345        7.458   3.741  -0.688
+ 19 20  PRO   3.287   4.031   1.686        4.025   4.206   2.856
+ 20 20  PRO   1.185   6.543  -0.353        0.358   5.421  -0.430
+ 21 12  SER   0.852  10.027   1.285        1.151  10.636   1.488
+ 22 21  D    -1.250  12.539  -0.754       -1.250  12.539  -0.754
+nsup= 20 nstart_sup=  2
+ ITEL
+           1          21           0
+           2          14           1
+           3           5           1
+           4           8           1
+           5           4           1
+           6          13           1
+           7           7           1
+           8           5           1
+           9          19           1
+          10          16           1
+          11          10           1
+          12          10           2
+          13          20           1
+          14          12           1
+          15          12           1
+          16          10           1
+          17          18           2
+          18          20           2
+          19          20           2
+          20          20           1
+          21          12           0
+ ns=           0  iss:
+Boundaries in phi angle sampling:
+D      1    -180.0     180.0
+ASN    2    -180.0     180.0
+LEU    3    -180.0     180.0
+TYR    4    -180.0     180.0
+ILE    5    -180.0     180.0
+GLN    6    -180.0     180.0
+TRP    7    -180.0     180.0
+LEU    8    -180.0     180.0
+LYS    9    -180.0     180.0
+ASP   10    -180.0     180.0
+GLY   11    -180.0     180.0
+GLY   12    -180.0     180.0
+PRO   13    -180.0     180.0
+SER   14    -180.0     180.0
+SER   15    -180.0     180.0
+GLY   16    -180.0     180.0
+ARG   17    -180.0     180.0
+PRO   18    -180.0     180.0
+PRO   19    -180.0     180.0
+PRO   20    -180.0     180.0
+SER   21    -180.0     180.0
+D     22    -180.0     180.0
+nsup= 20
+ nsup=          20  nstart_sup=           2  nstart_seq=           2
+ NZ_START=           2  NZ_END=          21
+ IZ_SC=           0
+ Contact order:  0.308441558441558     
+ Shifting contacts:           2           2
+           1  ILE            5  ASN            2
+           2  TRP            7  TYR            4
+           3  LEU            8  TYR            4
+           4  LEU            8  ILE            5
+           5  LYS            9  GLN            6
+           6  GLY           12  TRP            7
+           7  GLY           12  LEU            8
+           8  SER           14  GLY           11
+           9  SER           15  ASP           10
+          10  SER           15  GLY           11
+          11  PRO           19  TRP            7
+          12  PRO           20  LEU            3
+          13  PRO           20  TYR            4
+          14  PRO           20  TRP            7
+Initial geometry will be read in.
+
+Geometry of the virtual chain.
+  Res           d     Theta     Gamma       Dsc     Alpha      Beta 
+D     1     0.000     0.000     0.000     0.000     0.000     0.000
+ASN   2     3.800     0.000     0.000     1.684   102.356   -82.317
+LEU   3     3.800   104.929     0.000     1.939   120.092   -56.685
+TYR   4     3.800    87.695  -100.430     2.484   152.364    85.090
+ILE   5     3.800    81.904    72.426     1.776   134.976   -88.666
+GLN   6     3.800    82.466    66.026     2.240   122.343  -140.945
+TRP   7     3.800    84.466    51.434     2.605   152.178    38.024
+LEU   8     3.800    83.945    53.508     1.939   159.052   179.471
+LYS   9     3.800    85.396    60.569     2.541   100.558   -73.090
+ASP  10     3.800    91.449    44.177     1.709   139.961  -144.797
+GLY  11     3.800    94.602    67.604     0.000     0.000     0.000
+GLY  12     3.800   101.862   -72.814     0.000     0.000     0.000
+PRO  13     3.800   119.363   -61.916     1.345   117.453  -133.163
+SER  14     3.800    94.363   -75.894     1.150   137.025  -106.659
+SER  15     3.800    96.264    67.358     1.150   146.290  -130.305
+GLY  16     3.800   138.119   129.701     0.000     0.000     0.000
+ARG  17     3.800    96.299   -95.571     3.020    93.901  -102.747
+PRO  18     3.800   129.702    63.972     1.345   101.025  -111.641
+PRO  19     3.800   109.445   -74.504     1.345   113.043  -122.044
+PRO  20     3.800   106.349  -122.306     1.345    93.778  -102.374
+SER  21     3.800   106.042  -134.605     1.150   153.835  -143.303
+D    22     3.800   108.718    92.113     0.000     0.000     0.000
+Energy evaluation or minimization calculation.
+
+Conformations will be energy-minimized.
+********************************************************************************
+
+ Time for energy evaluation  0.000000000000000E+000
+
+Virtual-chain energies:
+
+EVDW=     -4.954316E+01 WEIGHT=    1.352790D+00 (SC-SC)
+EVDW2=     5.228224E+01 WEIGHT=    1.593040D+00 (SC-p)
+EES=      -1.132072E+02 WEIGHT=    7.153400D-01 (p-p)
+EVDWPP=    2.375178E+01 WEIGHT=    1.137100D-01 (p-p VDW)
+ESTR=      6.779273E-27 WEIGHT=    1.000000D+00 (stretching)
+EBE=      -1.651995E+01 WEIGHT=    1.138730D+00 (bending)
+ESC=       7.185904E+01 WEIGHT=    1.625800D-01 (SC local)
+ETORS=     8.243370E+00 WEIGHT=    1.985990D+00 (torsional)
+ETORSD=    2.390466E+00 WEIGHT=    1.570690D+00 (double torsional)
+EHBP=      0.000000E+00 WEIGHT=    1.000000D+00 (SS bridges & dist. cnstr.)
+ECORR4=   -8.338619E+01 WEIGHT=    4.288700D-01 (multi-body)
+ECORR5=    0.000000E+00 WEIGHT=    0.000000D+00 (multi-body)
+ECORR6=    0.000000E+00 WEIGHT=    0.000000D+00 (multi-body)
+EELLO=    -5.753258E+00 WEIGHT=    1.603600D-01 (electrostatic-local)
+ETURN3=    1.901845E+01 WEIGHT=    1.687220D+00 (turns, 3rd order)
+ETURN4=   -7.304754E+00 WEIGHT=    6.623000D-01 (turns, 4th order)
+ETURN6=    0.000000E+00 WEIGHT=    0.000000D+00 (turns, 6th order)
+ESCCOR=    0.000000E+00 WEIGHT=    0.000000D+00 (backbone-rotamer corr)
+EDIHC=     0.000000E+00 (dihedral angle constraints)
+ESS=       0.000000E+00 (disulfide-bridge intrinsic energy)
+UCONST=     0.000000E+00 (Constraint energy)
+ETOT=     -5.845169E+01 (total)
+PP contact map:
+  1  ASN   2  TYR   4
+  2  ASN   2  ILE   5
+  3  LEU   3  ILE   5
+  4  LEU   3  GLN   6
+  5  TYR   4  GLN   6
+  6  TYR   4  TRP   7
+  7  TYR   4  LEU   8
+  8  ILE   5  TRP   7
+  9  ILE   5  LEU   8
+ 10  GLN   6  LEU   8
+ 11  GLN   6  LYS   9
+ 12  TRP   7  LYS   9
+ 13  TRP   7  ASP  10
+ 14  TRP   7  GLY  11
+ 15  TRP   7  GLY  12
+ 16  LEU   8  ASP  10
+ 17  LEU   8  GLY  11
+ 18  LYS   9  GLY  11
+ 19  ASP  10  GLY  12
+ 20  GLY  11  PRO  13
+ 21  GLY  11  SER  14
+ 22  GLY  12  SER  14
+ 23  SER  14  GLY  16
+ 24  SER  15  ARG  17
+ 25  GLY  16  PRO  18
+ 26  ARG  17  PRO  19
+ 27  PRO  18  PRO  20
+ Hairpins:
+Constants of electrostatic interaction energy expression.
+ 1 1     0.7659E+08    -0.1823E+05    -0.1306E+04     0.3727E+01
+ 1 2     0.4245E+08    -0.9703E+04    -0.1129E+04     0.0000E+00
+ 2 1     0.4245E+08    -0.9703E+04    -0.1129E+04     0.0000E+00
+ 2 2     0.6367E+08    -0.1565E+05    -0.3348E+03     0.5127E+01
+ Total average electrostatic energy:   -17.0351458449875     
+ VDW energy between peptide-group centers:   -10.2064531653452     
+ 
+ Electrostatic contacts before pruning: 
+  1  ASN   2  TYR   4  -1.06027
+  2  LEU   3  ILE   5  -1.59865
+  3  LEU   3  GLN   6  -0.54360
+  4  TYR   4  GLN   6  -2.10033
+  5  TYR   4  TRP   7  -0.84900
+  6  ILE   5  TRP   7  -1.85979
+  7  ILE   5  LEU   8  -0.53540
+  8  GLN   6  LEU   8  -1.48363
+  9  GLN   6  LYS   9  -0.61868
+ 10  TRP   7  LYS   9  -1.55464
+ 11  TRP   7  GLY  12  -0.37651
+ 12  LEU   8  ASP  10  -0.61626
+ 13  LEU   8  GLY  11  -0.40662
+ 
+ Electrostatic contacts after pruning: 
+  1  ASN   2  TYR   4  -1.06027
+  2  LEU   3  ILE   5  -1.59865
+  3  LEU   3  GLN   6  -0.54360
+  4  TYR   4  GLN   6  -2.10033
+  5  TYR   4  TRP   7  -0.84900
+  6  ILE   5  TRP   7  -1.85979
+  7  ILE   5  LEU   8  -0.53540
+  8  GLN   6  LEU   8  -1.48363
+  9  GLN   6  LYS   9  -0.61868
+ 10  TRP   7  LYS   9  -1.55464
+ 11  TRP   7  GLY  12  -0.37651
+ 12  LEU   8  ASP  10  -0.61626
+ 13  LEU   8  GLY  11  -0.40662
+Helix  1   2  10
+ UNRES seq:
+ helix            3          11
+ SC_move        1190  -14.2312827671102     
+PP contact map:
+  1  ASN   2  TYR   4
+  2  ASN   2  ILE   5
+  3  LEU   3  ILE   5
+  4  LEU   3  GLN   6
+  5  LEU   3  TRP   7
+  6  TYR   4  GLN   6
+  7  TYR   4  TRP   7
+  8  TYR   4  LEU   8
+  9  ILE   5  TRP   7
+ 10  ILE   5  LEU   8
+ 11  ILE   5  LYS   9
+ 12  GLN   6  LEU   8
+ 13  GLN   6  LYS   9
+ 14  TRP   7  LYS   9
+ 15  TRP   7  ASP  10
+ 16  TRP   7  GLY  11
+ 17  TRP   7  GLY  12
+ 18  LEU   8  ASP  10
+ 19  LEU   8  GLY  11
+ 20  LYS   9  GLY  11
+ 21  ASP  10  GLY  12
+ 22  GLY  11  PRO  13
+ 23  GLY  11  SER  14
+ 24  GLY  12  SER  14
+ 25  PRO  13  SER  15
+ 26  SER  14  GLY  16
+ 27  SER  15  ARG  17
+ 28  PRO  18  PRO  20
+ Hairpins:
+Constants of electrostatic interaction energy expression.
+ 1 1     0.7659E+08    -0.1823E+05    -0.1306E+04     0.3727E+01
+ 1 2     0.4245E+08    -0.9703E+04    -0.1129E+04     0.0000E+00
+ 2 1     0.4245E+08    -0.9703E+04    -0.1129E+04     0.0000E+00
+ 2 2     0.6367E+08    -0.1565E+05    -0.3348E+03     0.5127E+01
+ Total average electrostatic energy:   -14.3281191505659     
+ VDW energy between peptide-group centers:   -22.1278543766753     
+ 
+ Electrostatic contacts before pruning: 
+  1  ASN   2  TYR   4  -0.80580
+  2  LEU   3  ILE   5  -1.08899
+  3  LEU   3  GLN   6  -0.51166
+  4  TYR   4  GLN   6  -1.35288
+  5  TYR   4  TRP   7  -0.71638
+  6  ILE   5  TRP   7  -1.25245
+  7  ILE   5  LEU   8  -0.56094
+  8  GLN   6  LEU   8  -1.12103
+  9  GLN   6  LYS   9  -0.52058
+ 10  TRP   7  LYS   9  -1.15119
+ 11  LEU   8  ASP  10  -0.71444
+ 12  LEU   8  GLY  11  -0.38113
+ 13  GLY  12  SER  14  -0.61187
+ 
+ Electrostatic contacts after pruning: 
+  1  ASN   2  TYR   4  -0.80580
+  2  LEU   3  ILE   5  -1.08899
+  3  LEU   3  GLN   6  -0.51166
+  4  TYR   4  GLN   6  -1.35288
+  5  TYR   4  TRP   7  -0.71638
+  6  ILE   5  TRP   7  -1.25245
+  7  ILE   5  LEU   8  -0.56094
+  8  GLN   6  LEU   8  -1.12103
+  9  GLN   6  LYS   9  -0.52058
+ 10  TRP   7  LYS   9  -1.15119
+ 11  LEU   8  ASP  10  -0.71444
+ 12  LEU   8  GLY  11  -0.38113
+ 13  GLY  12  SER  14  -0.61187
+Helix  1   2  10
+ UNRES seq:
+ helix            3          11
+
+Virtual-chain energies:
+
+EVDW=     -5.340090E+01 WEIGHT=    1.352790D+00 (SC-SC)
+EVDW2=     4.677947E+01 WEIGHT=    1.593040D+00 (SC-p)
+EES=      -9.503008E+01 WEIGHT=    7.153400D-01 (p-p)
+EVDWPP=   -2.608496E+01 WEIGHT=    1.137100D-01 (p-p VDW)
+ESTR=      6.779273E-27 WEIGHT=    1.000000D+00 (stretching)
+EBE=      -3.660091E+01 WEIGHT=    1.138730D+00 (bending)
+ESC=       8.674390E+01 WEIGHT=    1.625800D-01 (SC local)
+ETORS=     9.615105E+00 WEIGHT=    1.985990D+00 (torsional)
+ETORSD=    4.819701E-01 WEIGHT=    1.570690D+00 (double torsional)
+EHBP=      0.000000E+00 WEIGHT=    1.000000D+00 (SS bridges & dist. cnstr.)
+ECORR4=   -7.040856E+01 WEIGHT=    4.288700D-01 (multi-body)
+ECORR5=    0.000000E+00 WEIGHT=    0.000000D+00 (multi-body)
+ECORR6=    0.000000E+00 WEIGHT=    0.000000D+00 (multi-body)
+EELLO=    -7.334513E+00 WEIGHT=    1.603600D-01 (electrostatic-local)
+ETURN3=    1.856553E+01 WEIGHT=    1.687220D+00 (turns, 3rd order)
+ETURN4=   -3.312436E+00 WEIGHT=    6.623000D-01 (turns, 4th order)
+ETURN6=    0.000000E+00 WEIGHT=    0.000000D+00 (turns, 6th order)
+ESCCOR=    0.000000E+00 WEIGHT=    0.000000D+00 (backbone-rotamer corr)
+EDIHC=     0.000000E+00 (dihedral angle constraints)
+ESS=       0.000000E+00 (disulfide-bridge intrinsic energy)
+UCONST=     0.000000E+00 (Constraint energy)
+ETOT=     -7.862875E+01 (total)
+
+Geometry of the virtual chain.
+  Res           d     Theta     Gamma       Dsc     Alpha      Beta 
+D     1     0.000     0.000     0.000     0.000     0.000     0.000
+ASN   2     3.800     0.000     0.000     1.684   110.702   -85.685
+LEU   3     3.800   118.494     0.000     1.939   141.228   -49.540
+TYR   4     3.800    91.717  -100.428     2.484   118.549   113.868
+ILE   5     3.800    90.036    63.646     1.776   146.652   -96.973
+GLN   6     3.800    89.040    55.793     2.240   104.893   -50.566
+TRP   7     3.800    90.433    45.276     2.605   138.711    59.219
+LEU   8     3.800    90.769    45.241     1.939   136.395  -145.480
+LYS   9     3.800    90.500    50.320     2.541   134.179  -136.318
+ASP  10     3.800    92.103    46.289     1.709   143.475  -124.446
+GLY  11     3.800    91.360    65.751     0.000   180.000   180.000
+GLY  12     3.800   111.681   -71.670     0.000   180.000   180.000
+PRO  13     3.800   113.684   -58.655     1.345   129.775  -154.011
+SER  14     3.800    93.263   -78.152     1.150   115.010   -77.057
+SER  15     3.800    93.932    57.849     1.150   124.898  -144.294
+GLY  16     3.800   115.865   137.415     0.000   180.000   180.000
+ARG  17     3.800    94.303   -84.359     3.020    90.176  -107.687
+PRO  18     3.800   121.756    61.635     1.345   116.339  -177.378
+PRO  19     3.800   117.856   -81.085     1.345   141.987  -158.715
+PRO  20     3.800   115.623  -108.327     1.345    97.877   -97.653
+SER  21     3.800    93.855  -137.450     1.150   144.130  -129.546
+D    22     3.800   117.793    46.049     0.000   180.000   180.000
+RMS deviation from the reference structure:   2.067
+ % of native contacts:  78.571
+ % of nonnative contacts:  54.167
+ contact order:   0.348
+SUMSL return code:  4
+# of energy evaluations:                 348
+# of energy evaluations/sec:        3154.545
+
+
+***** Computation time:    0 hours  0 minutes  0 seconds *****

diff --git a/examples/unres/MD/ff_gab/1L2Y_minim.out_GB000 b/examples/unres/MD/ff_gab/1L2Y_minim.out_GB000
new file mode 100644 (file)
index 0000000..adbd935
--- /dev/null
+++ b/examples/unres/MD/ff_gab/1L2Y_minim.out_GB000
@@ -0,0 +1,494 @@
+--------------------------------------------------------------------------------
+                              FILE ASSIGNMENT
+--------------------------------------------------------------------------------
+ Input file                      : 1L2Y_minim.inp
+ Output file                     : 1L2Y_minim.out_GB000
+ 
+ Sidechain potential file        : 
+ /users/adam/UNRES/PARAM/sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16-10-8k
+ SCp potential file              : /users/adam/UNRES/PARAM/scp.parm
+ Electrostatic potential file    : /users/adam/UNRES/PARAM/electr_631Gdp.parm
+ Cumulant coefficient file       : 
+ /users/adam/UNRES/PARAM/fourier_opt.parm.1igd_hc_iter3_3
+ Torsional parameter file        : /users/adam/UNRES/PARAM/torsion_631Gdp.parm
+ Double torsional parameter file : 
+ /users/adam/UNRES/PARAM/torsion_double_631Gdp.parm
+ SCCOR parameter file : /users/adam/UNRES/PARAM/rotcorr_AM1.parm
+ Bond & inertia constant file    : /users/adam/UNRES/PARAM/bond.parm
+ Bending parameter file          : /users/adam/UNRES/PARAM/thetaml.5parm
+ Rotamer parameter file          : /users/adam/UNRES/PARAM/scgauss.parm
+ Threading database              : /users/adam/UNRES/PARAM/patterns.cart
+--------------------------------------------------------------------------------
+********************************************************************************
+United-residue force field calculation - parallel job.
+********************************************************************************
+ ### LAST MODIFIED  03/28/12 23:29 by czarek
+ ++++ Compile info ++++
+ Version 2.5 build 62
+ compiled Sun May 13 16:07:22 2012
+ compiled by adam@matrix.chem.cornell.edu
+ OS name:    Linux 
+ OS release: 2.6.34.9-69.fc13.x86_64 
+ OS version: #1 SMP Tue May 3 09:23:03 UTC 2011 
+ flags:
+ INSTALL_DIR = /users/software/mpich-1.2.7p1_int...
+ FC= ifort
+ OPT =  -O3 -ip -w 
+ 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 ...
+ LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf/libxdr...
+ ARCH = LINUX
+ PP = /lib/cpp -P
+ object = unres.o arcos.o cartprint.o chainbuild...
+ GAB: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNRES ...
+ GAB: BIN = ../../../bin/unres/MD/unres_ifort_MP...
+ E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNR...
+ E0LL2Y: BIN = ../../../bin/unres/MD/unres_ifort...
+ ++++ End of compile info ++++
+
+Potential is GB , exponents are   6 12
+
+Disulfide bridge parameters:
+S-S bridge energy:      -5.50
+d0cm:      3.78 akcm:     15.10
+akth:     11.00 akct:     12.00
+v1ss:     -1.08 v2ss:      7.61 v3ss:     13.70
+ MPI: node=            0  iseed(4)=            0           0         -46
+      -45086
+ ran_num  6.422640197456531E-013
+RMSDBC =        3.0
+RMSDBC1 =        0.5
+RMSDBC1MAX =        1.5
+DRMS    =        0.1
+RMSDBCM =        3.0
+Time limit (min):     960.0
+ RESCALE_MODE           1
+Library  routine used to diagonalize matrices.
+
+********************************************************************************
+                    Options in energy minimization:
+********************************************************************************
+MaxMin: 2000 MaxFun: 5000MinMin: 2000 MinFun: 2000 TolF:   1.00000E-02 RTolF:   1.00000E-04
+
+Energy-term weights (unscaled):
+
+WSCC=     1.352790 (SC-SC)
+WSCP=     1.593040 (SC-p)
+WELEC=    0.715340 (p-p electr)
+WVDWPP=   0.113710 (p-p VDW)
+WBOND=    1.000000 (stretching)
+WANG=     1.138730 (bending)
+WSCLOC=   0.162580 (SC local)
+WTOR=     1.985990 (torsional)
+WTORD=    1.570690 (double torsional)
+WSTRAIN=  1.000000 (SS bridges & dist. cnstr.)
+WEL_LOC=  0.160360 (multi-body 3-rd order)
+WCORR4=   0.428870 (multi-body 4th order)
+WCORR5=   0.000000 (multi-body 5th order)
+WCORR6=   0.000000 (multi-body 6th order)
+WSCCOR=   0.000000 (back-scloc correlation)
+WTURN3=   1.687220 (turns, 3rd order)
+WTURN4=   0.662300 (turns, 4th order)
+WTURN6=   0.000000 (turns, 6th order)
+
+Hydrogen-bonding correlation between contact pairs of peptide groups
+
+Scaling factor of 1,4 SC-p interactions:   0.400
+General scaling factor of SC-p interactions:   1.000
+
+Energy-term weights (scaled):
+
+WSCC=     1.352790 (SC-SC)
+WSCP=     1.593040 (SC-p)
+WELEC=    0.715340 (p-p electr)
+WVDWPP=   0.113710 (p-p VDW)
+WBOND=    1.000000 (stretching)
+WANG=     1.138730 (bending)
+WSCLOC=   0.162580 (SC local)
+WTOR=     1.985990 (torsional)
+WTORD=    1.570690 (double torsional)
+WSTRAIN=  1.000000 (SS bridges & dist. cnstr.)
+WEL_LOC=  0.160360 (multi-body 3-rd order)
+WCORR4=   0.428870 (multi-body 4th order)
+WCORR5=   0.000000 (multi-body 5th order)
+WCORR6=   0.000000 (multi-body 6th order)
+WSCCOR=   0.000000 (back-scloc correlatkion)
+WTURN3=   1.687220 (turns, 3rd order)
+WTURN4=   0.662300 (turns, 4th order)
+WTURN6=   0.000000 (turns, 6th order)
+ Reference temperature for weights calculation:   300.000000000000     
+ Parameters of the SS-bond potential:
+ D0CM   3.78000000000000       AKCM   15.1000000000000       AKTH
+   11.0000000000000       AKCT   12.0000000000000     
+ V1SS  -1.08000000000000       V2SS   7.61000000000000       V3SS
+   13.7000000000000     
+ EBR  -5.50000000000000     
+PDB data will be read from file 1L2Y.pdb
+ Nres:    21
+Backbone and SC coordinates as read from the PDB
+  1 21  D    -9.841   4.399  -5.051       -9.841   4.399  -5.051
+  2 14  ASN  -8.608   3.135  -1.618      -10.407   3.153  -2.437
+  3  5  LEU  -4.923   4.002  -2.452       -4.618   6.091  -1.850
+  4  8  TYR  -3.690   2.738   0.981       -1.959   3.143   3.797
+  5  4  ILE  -5.857  -0.449   0.613       -7.484  -0.369   1.074
+  6 13  GLN  -4.122  -1.167  -2.743       -5.089  -1.450  -4.853
+  7  7  TRP  -0.716  -0.631  -0.993        1.727   0.440   1.450
+  8  5  LEU  -1.641  -2.932   1.963       -2.244  -2.097   3.799
+  9 19  LYS  -3.024  -5.791  -0.269       -3.820  -5.527  -3.146
+ 10 16  ASP   0.466  -6.016  -1.905        0.653  -5.125  -3.676
+ 11 10  GLY   2.060  -6.618   1.593        2.060  -6.618   1.593
+ 12 10  GLY   2.626  -2.967   2.723        2.626  -2.967   2.723
+ 13 20  PRO   6.333  -2.533   3.806        5.724  -2.372   5.058
+ 14 12  SER   7.049  -6.179   2.704        6.757  -6.938   3.675
+ 15 12  SER   6.389  -5.315  -1.015        5.245  -5.350  -1.546
+ 16 10  GLY   9.451  -3.116  -1.870        9.451  -3.116  -1.870
+ 17 18  ARG   7.289   0.084  -2.054        5.225  -1.826  -3.986
+ 18 20  PRO   6.782   3.088   0.345        7.458   3.741  -0.688
+ 19 20  PRO   3.287   4.031   1.686        4.025   4.206   2.856
+ 20 20  PRO   1.185   6.543  -0.353        0.358   5.421  -0.430
+ 21 12  SER   0.852  10.027   1.285        1.151  10.636   1.488
+ 22 21  D    -1.250  12.539  -0.754       -1.250  12.539  -0.754
+nsup= 20 nstart_sup=  2
+ ITEL
+           1          21           0
+           2          14           1
+           3           5           1
+           4           8           1
+           5           4           1
+           6          13           1
+           7           7           1
+           8           5           1
+           9          19           1
+          10          16           1
+          11          10           1
+          12          10           2
+          13          20           1
+          14          12           1
+          15          12           1
+          16          10           1
+          17          18           2
+          18          20           2
+          19          20           2
+          20          20           1
+          21          12           0
+ ns=           0  iss:
+Boundaries in phi angle sampling:
+D      1    -180.0     180.0
+ASN    2    -180.0     180.0
+LEU    3    -180.0     180.0
+TYR    4    -180.0     180.0
+ILE    5    -180.0     180.0
+GLN    6    -180.0     180.0
+TRP    7    -180.0     180.0
+LEU    8    -180.0     180.0
+LYS    9    -180.0     180.0
+ASP   10    -180.0     180.0
+GLY   11    -180.0     180.0
+GLY   12    -180.0     180.0
+PRO   13    -180.0     180.0
+SER   14    -180.0     180.0
+SER   15    -180.0     180.0
+GLY   16    -180.0     180.0
+ARG   17    -180.0     180.0
+PRO   18    -180.0     180.0
+PRO   19    -180.0     180.0
+PRO   20    -180.0     180.0
+SER   21    -180.0     180.0
+D     22    -180.0     180.0
+nsup= 20
+ nsup=          20  nstart_sup=           2  nstart_seq=           2
+ NZ_START=           2  NZ_END=          21
+ IZ_SC=           0
+ Contact order:  0.308441558441558     
+ Shifting contacts:           2           2
+           1  ILE            5  ASN            2
+           2  TRP            7  TYR            4
+           3  LEU            8  TYR            4
+           4  LEU            8  ILE            5
+           5  LYS            9  GLN            6
+           6  GLY           12  TRP            7
+           7  GLY           12  LEU            8
+           8  SER           14  GLY           11
+           9  SER           15  ASP           10
+          10  SER           15  GLY           11
+          11  PRO           19  TRP            7
+          12  PRO           20  LEU            3
+          13  PRO           20  TYR            4
+          14  PRO           20  TRP            7
+Initial geometry will be read in.
+
+Geometry of the virtual chain.
+  Res           d     Theta     Gamma       Dsc     Alpha      Beta 
+D     1     0.000     0.000     0.000     0.000     0.000     0.000
+ASN   2     3.800     0.000     0.000     1.684   102.356   -82.317
+LEU   3     3.800   104.929     0.000     1.939   120.092   -56.685
+TYR   4     3.800    87.695  -100.430     2.484   152.364    85.090
+ILE   5     3.800    81.904    72.426     1.776   134.976   -88.666
+GLN   6     3.800    82.466    66.026     2.240   122.343  -140.945
+TRP   7     3.800    84.466    51.434     2.605   152.178    38.024
+LEU   8     3.800    83.945    53.508     1.939   159.052   179.471
+LYS   9     3.800    85.396    60.569     2.541   100.558   -73.090
+ASP  10     3.800    91.449    44.177     1.709   139.961  -144.797
+GLY  11     3.800    94.602    67.604     0.000     0.000     0.000
+GLY  12     3.800   101.862   -72.814     0.000     0.000     0.000
+PRO  13     3.800   119.363   -61.916     1.345   117.453  -133.163
+SER  14     3.800    94.363   -75.894     1.150   137.025  -106.659
+SER  15     3.800    96.264    67.358     1.150   146.290  -130.305
+GLY  16     3.800   138.119   129.701     0.000     0.000     0.000
+ARG  17     3.800    96.299   -95.571     3.020    93.901  -102.747
+PRO  18     3.800   129.702    63.972     1.345   101.025  -111.641
+PRO  19     3.800   109.445   -74.504     1.345   113.043  -122.044
+PRO  20     3.800   106.349  -122.306     1.345    93.778  -102.374
+SER  21     3.800   106.042  -134.605     1.150   153.835  -143.303
+D    22     3.800   108.718    92.113     0.000     0.000     0.000
+
+
+********************************************************************************
+                    Processor   0: end reading molecular data.
+********************************************************************************
+
+
+Energy evaluation or minimization calculation.
+
+Conformations will be energy-minimized.
+********************************************************************************
+
+ Time for energy evaluation  0.000000000000000E+000
+
+Virtual-chain energies:
+
+EVDW=     -4.954316E+01 WEIGHT=    1.352790D+00 (SC-SC)
+EVDW2=     5.228224E+01 WEIGHT=    1.593040D+00 (SC-p)
+EES=      -1.132072E+02 WEIGHT=    7.153400D-01 (p-p)
+EVDWPP=    2.375178E+01 WEIGHT=    1.137100D-01 (p-p VDW)
+ESTR=      6.779273E-27 WEIGHT=    1.000000D+00 (stretching)
+EBE=      -1.651995E+01 WEIGHT=    1.138730D+00 (bending)
+ESC=       7.185904E+01 WEIGHT=    1.625800D-01 (SC local)
+ETORS=     8.243370E+00 WEIGHT=    1.985990D+00 (torsional)
+ETORSD=    2.390466E+00 WEIGHT=    1.570690D+00 (double torsional)
+EHPB=      0.000000E+00 WEIGHT=    1.000000D+00 (SS bridges & dist. cnstr.)
+ECORR4=   -8.338619E+01 WEIGHT=    4.288700D-01 (multi-body)
+ECORR5=    0.000000E+00 WEIGHT=    0.000000D+00 (multi-body)
+ECORR6=    0.000000E+00 WEIGHT=    0.000000D+00 (multi-body)
+EELLO=    -5.753258E+00 WEIGHT=    1.603600D-01 (electrostatic-local)
+ETURN3=    1.901845E+01 WEIGHT=    1.687220D+00 (turns, 3rd order)
+ETURN4=   -7.304754E+00 WEIGHT=    6.623000D-01 (turns, 4th order)
+ETURN6=    0.000000E+00 WEIGHT=    0.000000D+00 (turns, 6th order)
+ESCCOR=    0.000000E+00 WEIGHT=    0.000000D+00 (backbone-rotamer corr)
+EDIHC=     0.000000E+00 (dihedral angle constraints)
+ESS=       0.000000E+00 (disulfide-bridge intrinsic energy)
+UCONST=     0.000000E+00 (Constraint energy)
+ETOT=     -5.845169E+01 (total)
+PP contact map:
+  1  ASN   2  TYR   4
+  2  ASN   2  ILE   5
+  3  LEU   3  ILE   5
+  4  LEU   3  GLN   6
+  5  TYR   4  GLN   6
+  6  TYR   4  TRP   7
+  7  TYR   4  LEU   8
+  8  ILE   5  TRP   7
+  9  ILE   5  LEU   8
+ 10  GLN   6  LEU   8
+ 11  GLN   6  LYS   9
+ 12  TRP   7  LYS   9
+ 13  TRP   7  ASP  10
+ 14  TRP   7  GLY  11
+ 15  TRP   7  GLY  12
+ 16  LEU   8  ASP  10
+ 17  LEU   8  GLY  11
+ 18  LYS   9  GLY  11
+ 19  ASP  10  GLY  12
+ 20  GLY  11  PRO  13
+ 21  GLY  11  SER  14
+ 22  GLY  12  SER  14
+ 23  SER  14  GLY  16
+ 24  SER  15  ARG  17
+ 25  GLY  16  PRO  18
+ 26  ARG  17  PRO  19
+ 27  PRO  18  PRO  20
+ Hairpins:
+Constants of electrostatic interaction energy expression.
+ 1 1     0.7659E+08    -0.1823E+05    -0.1306E+04     0.3727E+01
+ 1 2     0.4245E+08    -0.9703E+04    -0.1129E+04     0.0000E+00
+ 2 1     0.4245E+08    -0.9703E+04    -0.1129E+04     0.0000E+00
+ 2 2     0.6367E+08    -0.1565E+05    -0.3348E+03     0.5127E+01
+ Total average electrostatic energy:   -17.0351458449875     
+ VDW energy between peptide-group centers:   -10.2064531653452     
+ 
+ Electrostatic contacts before pruning: 
+  1  ASN   2  TYR   4  -1.06027
+  2  LEU   3  ILE   5  -1.59865
+  3  LEU   3  GLN   6  -0.54360
+  4  TYR   4  GLN   6  -2.10033
+  5  TYR   4  TRP   7  -0.84900
+  6  ILE   5  TRP   7  -1.85979
+  7  ILE   5  LEU   8  -0.53540
+  8  GLN   6  LEU   8  -1.48363
+  9  GLN   6  LYS   9  -0.61868
+ 10  TRP   7  LYS   9  -1.55464
+ 11  TRP   7  GLY  12  -0.37651
+ 12  LEU   8  ASP  10  -0.61626
+ 13  LEU   8  GLY  11  -0.40662
+ 
+ Electrostatic contacts after pruning: 
+  1  ASN   2  TYR   4  -1.06027
+  2  LEU   3  ILE   5  -1.59865
+  3  LEU   3  GLN   6  -0.54360
+  4  TYR   4  GLN   6  -2.10033
+  5  TYR   4  TRP   7  -0.84900
+  6  ILE   5  TRP   7  -1.85979
+  7  ILE   5  LEU   8  -0.53540
+  8  GLN   6  LEU   8  -1.48363
+  9  GLN   6  LYS   9  -0.61868
+ 10  TRP   7  LYS   9  -1.55464
+ 11  TRP   7  GLY  12  -0.37651
+ 12  LEU   8  ASP  10  -0.61626
+ 13  LEU   8  GLY  11  -0.40662
+Helix  1   2  10
+ UNRES seq:
+ helix            3          11
+ SC_move        1190  -36.8538206659302     
+PP contact map:
+  1  ASN   2  TYR   4
+  2  ASN   2  ILE   5
+  3  LEU   3  ILE   5
+  4  LEU   3  GLN   6
+  5  LEU   3  TRP   7
+  6  LEU   3  LEU   8
+  7  TYR   4  GLN   6
+  8  TYR   4  TRP   7
+  9  TYR   4  LEU   8
+ 10  ILE   5  TRP   7
+ 11  ILE   5  LEU   8
+ 12  ILE   5  LYS   9
+ 13  GLN   6  LEU   8
+ 14  GLN   6  LYS   9
+ 15  TRP   7  LYS   9
+ 16  TRP   7  ASP  10
+ 17  TRP   7  GLY  11
+ 18  TRP   7  GLY  12
+ 19  LEU   8  ASP  10
+ 20  LEU   8  GLY  11
+ 21  LEU   8  GLY  12
+ 22  LYS   9  GLY  11
+ 23  ASP  10  GLY  12
+ 24  ASP  10  PRO  13
+ 25  ASP  10  SER  14
+ 26  GLY  11  PRO  13
+ 27  GLY  11  SER  14
+ 28  GLY  12  SER  14
+ 29  PRO  13  SER  15
+ 30  SER  14  GLY  16
+ 31  SER  15  ARG  17
+ 32  PRO  18  PRO  20
+ Hairpins:
+Constants of electrostatic interaction energy expression.
+ 1 1     0.7659E+08    -0.1823E+05    -0.1306E+04     0.3727E+01
+ 1 2     0.4245E+08    -0.9703E+04    -0.1129E+04     0.0000E+00
+ 2 1     0.4245E+08    -0.9703E+04    -0.1129E+04     0.0000E+00
+ 2 2     0.6367E+08    -0.1565E+05    -0.3348E+03     0.5127E+01
+ Total average electrostatic energy:   -37.0692889481661     
+ VDW energy between peptide-group centers:    851.859545972044     
+ 
+ Electrostatic contacts before pruning: 
+  1  ASN   2  TYR   4  -9.86113
+  2  ASN   2  ILE   5  -1.53124
+  3  LEU   3  ILE   5 -10.58267
+  4  LEU   3  GLN   6  -1.25110
+  5  LEU   3  TRP   7  -0.80052
+  6  TYR   4  GLN   6  -1.33813
+  7  TYR   4  TRP   7  -0.75936
+  8  ILE   5  TRP   7  -1.25974
+  9  ILE   5  LEU   8  -0.55583
+ 10  GLN   6  LEU   8  -1.12670
+ 11  GLN   6  LYS   9  -0.55504
+ 12  TRP   7  LYS   9  -1.20931
+ 13  TRP   7  GLY  12  -0.39500
+ 14  LEU   8  ASP  10  -0.66375
+ 15  LEU   8  GLY  11  -0.49451
+ 16  ASP  10  SER  14  -0.49993
+ 17  GLY  11  PRO  13  -0.96815
+ 
+ Electrostatic contacts after pruning: 
+  1  ASN   2  TYR   4  -9.86113
+  2  ASN   2  ILE   5  -1.53124
+  3  LEU   3  ILE   5 -10.58267
+  4  LEU   3  GLN   6  -1.25110
+  5  LEU   3  TRP   7  -0.80052
+  6  TYR   4  GLN   6  -1.33813
+  7  TYR   4  TRP   7  -0.75936
+  8  ILE   5  TRP   7  -1.25974
+  9  ILE   5  LEU   8  -0.55583
+ 10  GLN   6  LEU   8  -1.12670
+ 11  GLN   6  LYS   9  -0.55504
+ 12  TRP   7  LYS   9  -1.20931
+ 13  TRP   7  GLY  12  -0.39500
+ 14  LEU   8  ASP  10  -0.66375
+ 15  LEU   8  GLY  11  -0.49451
+ 16  ASP  10  SER  14  -0.49993
+ 17  GLY  11  PRO  13  -0.96815
+Helix  1   3  10
+ UNRES seq:
+ helix            4          11
+
+Virtual-chain energies:
+
+EVDW=      1.906975E+22 WEIGHT=    1.352790D+00 (SC-SC)
+EVDW2=     2.099470E+04 WEIGHT=    1.593040D+00 (SC-p)
+EES=      -2.515997E+02 WEIGHT=    7.153400D-01 (p-p)
+EVDWPP=    2.987216E+03 WEIGHT=    1.137100D-01 (p-p VDW)
+ESTR=      6.779273E-27 WEIGHT=    1.000000D+00 (stretching)
+EBE=      -9.194128E+00 WEIGHT=    1.138730D+00 (bending)
+ESC=       5.035340E+32 WEIGHT=    1.625800D-01 (SC local)
+ETORS=     8.926809E+00 WEIGHT=    1.985990D+00 (torsional)
+ETORSD=   -4.669374E-01 WEIGHT=    1.570690D+00 (double torsional)
+EHPB=      0.000000E+00 WEIGHT=    1.000000D+00 (SS bridges & dist. cnstr.)
+ECORR4=   -1.345056E+02 WEIGHT=    4.288700D-01 (multi-body)
+ECORR5=    0.000000E+00 WEIGHT=    0.000000D+00 (multi-body)
+ECORR6=    0.000000E+00 WEIGHT=    0.000000D+00 (multi-body)
+EELLO=  NaN             WEIGHT=    1.603600D-01 (electrostatic-local)
+ETURN3= NaN             WEIGHT=    1.687220D+00 (turns, 3rd order)
+ETURN4= NaN             WEIGHT=    6.623000D-01 (turns, 4th order)
+ETURN6=    0.000000E+00 WEIGHT=    0.000000D+00 (turns, 6th order)
+ESCCOR=    0.000000E+00 WEIGHT=    0.000000D+00 (backbone-rotamer corr)
+EDIHC=     0.000000E+00 (dihedral angle constraints)
+ESS=       0.000000E+00 (disulfide-bridge intrinsic energy)
+UCONST=     0.000000E+00 (Constraint energy)
+ETOT=      1.000000E+99 (total)
+
+Geometry of the virtual chain.
+  Res           d     Theta     Gamma       Dsc     Alpha      Beta 
+D     1     0.000     0.000     0.000     0.000     0.000     0.000
+ASN   2     3.800     0.000     0.000     1.684    66.094   -81.746
+LEU   3     3.800   118.689     0.000     1.939   138.109   -26.893
+TYR   4     3.800    91.783  -149.590     2.484   123.984   108.154
+ILE   5     3.800     0.000    84.251     1.776   149.498   -90.988
+GLN   6     3.800    90.614    45.428     2.240   118.674  -118.972
+TRP   7     3.800    90.358    42.479     2.605   163.095    48.723
+LEU   8     3.800    90.561    45.576     1.939   145.280  -129.675
+LYS   9     3.800    90.389    50.728     2.541   133.176  -134.505
+ASP  10     3.800    91.852    44.664     1.709   133.932  -129.183
+GLY  11     3.800    90.570    70.394     0.000   180.000   180.000
+GLY  12     3.800   105.668   -67.487     0.000   180.000   180.000
+PRO  13     3.800    99.159   -65.573     1.345   115.572  -113.582
+SER  14     3.800    92.474   -33.144     1.150   113.504   -79.318
+SER  15     3.800    94.029   101.491     1.150   124.420  -158.647
+GLY  16     3.800   115.039   122.531     0.000   180.000   180.000
+ARG  17     3.800    94.980   -88.208     3.020   101.436  -102.179
+PRO  18     3.800   125.046    63.779     1.345   121.700  -130.547
+PRO  19     3.800   117.245   -83.662     1.345   110.939  -109.306
+PRO  20     3.800   121.153  -109.808     1.345   105.368  -111.814
+SER  21     3.800    92.281  -149.201     1.150   124.532  -120.711
+D    22     3.800   116.744   105.020     0.000   180.000   180.000
+RMS deviation from the reference structure:   2.344
+ % of native contacts:  64.286
+ % of nonnative contacts:  57.143
+ contact order:   0.253
+SUMSL return code:  4
+# of energy evaluations:                 553
+# of energy evaluations/sec:        3072.000
+CG processor   0 is finishing work.
+ Total wall clock time  0.242187500000000       sec

diff --git a/examples/unres/MD/ff_gab/1L2Y_minim.out_LJ000 b/examples/unres/MD/ff_gab/1L2Y_minim.out_LJ000
new file mode 100644 (file)
index 0000000..f1d12ca
--- /dev/null
+++ b/examples/unres/MD/ff_gab/1L2Y_minim.out_LJ000
@@ -0,0 +1,492 @@
+--------------------------------------------------------------------------------
+                              FILE ASSIGNMENT
+--------------------------------------------------------------------------------
+ Input file                      : 1L2Y_minim.inp
+ Output file                     : 1L2Y_minim.out_LJ000
+ 
+ Sidechain potential file        : /users/adam/UNRES/PARAM/scinter_LJ.parm
+ SCp potential file              : /users/adam/UNRES/PARAM/scp.parm
+ Electrostatic potential file    : /users/adam/UNRES/PARAM/electr_631Gdp.parm
+ Cumulant coefficient file       : 
+ /users/adam/UNRES/PARAM/fourier_opt.parm.1igd_hc_iter3_3
+ Torsional parameter file        : /users/adam/UNRES/PARAM/torsion_631Gdp.parm
+ Double torsional parameter file : 
+ /users/adam/UNRES/PARAM/torsion_double_631Gdp.parm
+ SCCOR parameter file : /users/adam/UNRES/PARAM/rotcorr_AM1.parm
+ Bond & inertia constant file    : /users/adam/UNRES/PARAM/bond.parm
+ Bending parameter file          : /users/adam/UNRES/PARAM/thetaml.5parm
+ Rotamer parameter file          : /users/adam/UNRES/PARAM/scgauss.parm
+ Threading database              : /users/adam/UNRES/PARAM/patterns.cart
+--------------------------------------------------------------------------------
+********************************************************************************
+United-residue force field calculation - parallel job.
+********************************************************************************
+ ### LAST MODIFIED  03/28/12 23:29 by czarek
+ ++++ Compile info ++++
+ Version 2.5 build 62
+ compiled Sun May 13 16:07:22 2012
+ compiled by adam@matrix.chem.cornell.edu
+ OS name:    Linux 
+ OS release: 2.6.34.9-69.fc13.x86_64 
+ OS version: #1 SMP Tue May 3 09:23:03 UTC 2011 
+ flags:
+ INSTALL_DIR = /users/software/mpich-1.2.7p1_int...
+ FC= ifort
+ OPT =  -O3 -ip -w 
+ 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 ...
+ LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf/libxdr...
+ ARCH = LINUX
+ PP = /lib/cpp -P
+ object = unres.o arcos.o cartprint.o chainbuild...
+ GAB: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNRES ...
+ GAB: BIN = ../../../bin/unres/MD/unres_ifort_MP...
+ E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNR...
+ E0LL2Y: BIN = ../../../bin/unres/MD/unres_ifort...
+ ++++ End of compile info ++++
+
+Potential is LJ , exponents are   6 12
+
+Disulfide bridge parameters:
+S-S bridge energy:      -5.50
+d0cm:      3.78 akcm:     15.10
+akth:     11.00 akct:     12.00
+v1ss:     -1.08 v2ss:      7.61 v3ss:     13.70
+ MPI: node=            0  iseed(4)=            0           0         -46
+      -45086
+ ran_num  6.422640197456531E-013
+RMSDBC =        3.0
+RMSDBC1 =        0.5
+RMSDBC1MAX =        1.5
+DRMS    =        0.1
+RMSDBCM =        3.0
+Time limit (min):     960.0
+ RESCALE_MODE           1
+Library  routine used to diagonalize matrices.
+
+********************************************************************************
+                    Options in energy minimization:
+********************************************************************************
+MaxMin: 2000 MaxFun: 5000MinMin: 2000 MinFun: 2000 TolF:   1.00000E-02 RTolF:   1.00000E-04
+
+Energy-term weights (unscaled):
+
+WSCC=     1.352790 (SC-SC)
+WSCP=     1.593040 (SC-p)
+WELEC=    0.715340 (p-p electr)
+WVDWPP=   0.113710 (p-p VDW)
+WBOND=    1.000000 (stretching)
+WANG=     1.138730 (bending)
+WSCLOC=   0.162580 (SC local)
+WTOR=     1.985990 (torsional)
+WTORD=    1.570690 (double torsional)
+WSTRAIN=  1.000000 (SS bridges & dist. cnstr.)
+WEL_LOC=  0.160360 (multi-body 3-rd order)
+WCORR4=   0.428870 (multi-body 4th order)
+WCORR5=   0.000000 (multi-body 5th order)
+WCORR6=   0.000000 (multi-body 6th order)
+WSCCOR=   0.000000 (back-scloc correlation)
+WTURN3=   1.687220 (turns, 3rd order)
+WTURN4=   0.662300 (turns, 4th order)
+WTURN6=   0.000000 (turns, 6th order)
+
+Hydrogen-bonding correlation between contact pairs of peptide groups
+
+Scaling factor of 1,4 SC-p interactions:   0.400
+General scaling factor of SC-p interactions:   1.000
+
+Energy-term weights (scaled):
+
+WSCC=     1.352790 (SC-SC)
+WSCP=     1.593040 (SC-p)
+WELEC=    0.715340 (p-p electr)
+WVDWPP=   0.113710 (p-p VDW)
+WBOND=    1.000000 (stretching)
+WANG=     1.138730 (bending)
+WSCLOC=   0.162580 (SC local)
+WTOR=     1.985990 (torsional)
+WTORD=    1.570690 (double torsional)
+WSTRAIN=  1.000000 (SS bridges & dist. cnstr.)
+WEL_LOC=  0.160360 (multi-body 3-rd order)
+WCORR4=   0.428870 (multi-body 4th order)
+WCORR5=   0.000000 (multi-body 5th order)
+WCORR6=   0.000000 (multi-body 6th order)
+WSCCOR=   0.000000 (back-scloc correlatkion)
+WTURN3=   1.687220 (turns, 3rd order)
+WTURN4=   0.662300 (turns, 4th order)
+WTURN6=   0.000000 (turns, 6th order)
+ Reference temperature for weights calculation:   300.000000000000     
+ Parameters of the SS-bond potential:
+ D0CM   3.78000000000000       AKCM   15.1000000000000       AKTH
+   11.0000000000000       AKCT   12.0000000000000     
+ V1SS  -1.08000000000000       V2SS   7.61000000000000       V3SS
+   13.7000000000000     
+ EBR  -5.50000000000000     
+PDB data will be read from file 1L2Y.pdb
+ Nres:    21
+Backbone and SC coordinates as read from the PDB
+  1 21  D    -9.841   4.399  -5.051       -9.841   4.399  -5.051
+  2 14  ASN  -8.608   3.135  -1.618      -10.407   3.153  -2.437
+  3  5  LEU  -4.923   4.002  -2.452       -4.618   6.091  -1.850
+  4  8  TYR  -3.690   2.738   0.981       -1.959   3.143   3.797
+  5  4  ILE  -5.857  -0.449   0.613       -7.484  -0.369   1.074
+  6 13  GLN  -4.122  -1.167  -2.743       -5.089  -1.450  -4.853
+  7  7  TRP  -0.716  -0.631  -0.993        1.727   0.440   1.450
+  8  5  LEU  -1.641  -2.932   1.963       -2.244  -2.097   3.799
+  9 19  LYS  -3.024  -5.791  -0.269       -3.820  -5.527  -3.146
+ 10 16  ASP   0.466  -6.016  -1.905        0.653  -5.125  -3.676
+ 11 10  GLY   2.060  -6.618   1.593        2.060  -6.618   1.593
+ 12 10  GLY   2.626  -2.967   2.723        2.626  -2.967   2.723
+ 13 20  PRO   6.333  -2.533   3.806        5.724  -2.372   5.058
+ 14 12  SER   7.049  -6.179   2.704        6.757  -6.938   3.675
+ 15 12  SER   6.389  -5.315  -1.015        5.245  -5.350  -1.546
+ 16 10  GLY   9.451  -3.116  -1.870        9.451  -3.116  -1.870
+ 17 18  ARG   7.289   0.084  -2.054        5.225  -1.826  -3.986
+ 18 20  PRO   6.782   3.088   0.345        7.458   3.741  -0.688
+ 19 20  PRO   3.287   4.031   1.686        4.025   4.206   2.856
+ 20 20  PRO   1.185   6.543  -0.353        0.358   5.421  -0.430
+ 21 12  SER   0.852  10.027   1.285        1.151  10.636   1.488
+ 22 21  D    -1.250  12.539  -0.754       -1.250  12.539  -0.754
+nsup= 20 nstart_sup=  2
+ ITEL
+           1          21           0
+           2          14           1
+           3           5           1
+           4           8           1
+           5           4           1
+           6          13           1
+           7           7           1
+           8           5           1
+           9          19           1
+          10          16           1
+          11          10           1
+          12          10           2
+          13          20           1
+          14          12           1
+          15          12           1
+          16          10           1
+          17          18           2
+          18          20           2
+          19          20           2
+          20          20           1
+          21          12           0
+ ns=           0  iss:
+Boundaries in phi angle sampling:
+D      1    -180.0     180.0
+ASN    2    -180.0     180.0
+LEU    3    -180.0     180.0
+TYR    4    -180.0     180.0
+ILE    5    -180.0     180.0
+GLN    6    -180.0     180.0
+TRP    7    -180.0     180.0
+LEU    8    -180.0     180.0
+LYS    9    -180.0     180.0
+ASP   10    -180.0     180.0
+GLY   11    -180.0     180.0
+GLY   12    -180.0     180.0
+PRO   13    -180.0     180.0
+SER   14    -180.0     180.0
+SER   15    -180.0     180.0
+GLY   16    -180.0     180.0
+ARG   17    -180.0     180.0
+PRO   18    -180.0     180.0
+PRO   19    -180.0     180.0
+PRO   20    -180.0     180.0
+SER   21    -180.0     180.0
+D     22    -180.0     180.0
+nsup= 20
+ nsup=          20  nstart_sup=           2  nstart_seq=           2
+ NZ_START=           2  NZ_END=          21
+ IZ_SC=           0
+ Contact order:  0.320158102766798     
+ Shifting contacts:           2           2
+           1  ILE            5  ASN            2
+           2  TRP            7  TYR            4
+           3  LEU            8  TYR            4
+           4  LEU            8  ILE            5
+           5  LYS            9  GLN            6
+           6  GLY           11  TRP            7
+           7  GLY           11  LEU            8
+           8  GLY           12  TRP            7
+           9  GLY           12  LEU            8
+          10  PRO           13  TRP            7
+          11  SER           14  GLY           11
+          12  SER           15  TRP            7
+          13  SER           15  ASP           10
+          14  SER           15  GLY           11
+          15  SER           15  GLY           12
+          16  ARG           17  TRP            7
+          17  ARG           17  ASP           10
+          18  PRO           18  TRP            7
+          19  PRO           19  TYR            4
+          20  PRO           19  TRP            7
+          21  PRO           20  LEU            3
+          22  PRO           20  TYR            4
+          23  PRO           20  TRP            7
+Initial geometry will be read in.
+
+Geometry of the virtual chain.
+  Res           d     Theta     Gamma       Dsc     Alpha      Beta 
+D     1     0.000     0.000     0.000     0.000     0.000     0.000
+ASN   2     3.800     0.000     0.000     1.684   102.356   -82.317
+LEU   3     3.800   104.929     0.000     1.939   120.092   -56.685
+TYR   4     3.800    87.695  -100.430     2.484   152.364    85.090
+ILE   5     3.800    81.904    72.426     1.776   134.976   -88.666
+GLN   6     3.800    82.466    66.026     2.240   122.343  -140.945
+TRP   7     3.800    84.466    51.434     2.605   152.178    38.024
+LEU   8     3.800    83.945    53.508     1.939   159.052   179.471
+LYS   9     3.800    85.396    60.569     2.541   100.558   -73.090
+ASP  10     3.800    91.449    44.177     1.709   139.961  -144.797
+GLY  11     3.800    94.602    67.604     0.000     0.000     0.000
+GLY  12     3.800   101.862   -72.814     0.000     0.000     0.000
+PRO  13     3.800   119.363   -61.916     1.345   117.453  -133.163
+SER  14     3.800    94.363   -75.894     1.150   137.025  -106.659
+SER  15     3.800    96.264    67.358     1.150   146.290  -130.305
+GLY  16     3.800   138.119   129.701     0.000     0.000     0.000
+ARG  17     3.800    96.299   -95.571     3.020    93.901  -102.747
+PRO  18     3.800   129.702    63.972     1.345   101.025  -111.641
+PRO  19     3.800   109.445   -74.504     1.345   113.043  -122.044
+PRO  20     3.800   106.349  -122.306     1.345    93.778  -102.374
+SER  21     3.800   106.042  -134.605     1.150   153.835  -143.303
+D    22     3.800   108.718    92.113     0.000     0.000     0.000
+
+
+********************************************************************************
+                    Processor   0: end reading molecular data.
+********************************************************************************
+
+
+Energy evaluation or minimization calculation.
+
+Conformations will be energy-minimized.
+********************************************************************************
+
+ Time for energy evaluation  0.000000000000000E+000
+
+Virtual-chain energies:
+
+EVDW=      6.950763E+00 WEIGHT=    1.352790D+00 (SC-SC)
+EVDW2=     5.228224E+01 WEIGHT=    1.593040D+00 (SC-p)
+EES=      -1.132072E+02 WEIGHT=    7.153400D-01 (p-p)
+EVDWPP=    2.375178E+01 WEIGHT=    1.137100D-01 (p-p VDW)
+ESTR=      6.779273E-27 WEIGHT=    1.000000D+00 (stretching)
+EBE=      -1.651995E+01 WEIGHT=    1.138730D+00 (bending)
+ESC=       7.185904E+01 WEIGHT=    1.625800D-01 (SC local)
+ETORS=     8.243370E+00 WEIGHT=    1.985990D+00 (torsional)
+ETORSD=    2.390466E+00 WEIGHT=    1.570690D+00 (double torsional)
+EHPB=      0.000000E+00 WEIGHT=    1.000000D+00 (SS bridges & dist. cnstr.)
+ECORR4=   -8.338619E+01 WEIGHT=    4.288700D-01 (multi-body)
+ECORR5=    0.000000E+00 WEIGHT=    0.000000D+00 (multi-body)
+ECORR6=    0.000000E+00 WEIGHT=    0.000000D+00 (multi-body)
+EELLO=    -5.753258E+00 WEIGHT=    1.603600D-01 (electrostatic-local)
+ETURN3=    1.901845E+01 WEIGHT=    1.687220D+00 (turns, 3rd order)
+ETURN4=   -7.304754E+00 WEIGHT=    6.623000D-01 (turns, 4th order)
+ETURN6=    0.000000E+00 WEIGHT=    0.000000D+00 (turns, 6th order)
+ESCCOR=    0.000000E+00 WEIGHT=    0.000000D+00 (backbone-rotamer corr)
+EDIHC=     0.000000E+00 (dihedral angle constraints)
+ESS=       0.000000E+00 (disulfide-bridge intrinsic energy)
+UCONST=     0.000000E+00 (Constraint energy)
+ETOT=      1.797273E+01 (total)
+PP contact map:
+  1  ASN   2  TYR   4
+  2  ASN   2  ILE   5
+  3  LEU   3  ILE   5
+  4  LEU   3  GLN   6
+  5  TYR   4  GLN   6
+  6  TYR   4  TRP   7
+  7  TYR   4  LEU   8
+  8  ILE   5  TRP   7
+  9  ILE   5  LEU   8
+ 10  GLN   6  LEU   8
+ 11  GLN   6  LYS   9
+ 12  TRP   7  LYS   9
+ 13  TRP   7  ASP  10
+ 14  TRP   7  GLY  11
+ 15  TRP   7  GLY  12
+ 16  LEU   8  ASP  10
+ 17  LEU   8  GLY  11
+ 18  LYS   9  GLY  11
+ 19  ASP  10  GLY  12
+ 20  GLY  11  PRO  13
+ 21  GLY  11  SER  14
+ 22  GLY  12  SER  14
+ 23  SER  14  GLY  16
+ 24  SER  15  ARG  17
+ 25  GLY  16  PRO  18
+ 26  ARG  17  PRO  19
+ 27  PRO  18  PRO  20
+ Hairpins:
+Constants of electrostatic interaction energy expression.
+ 1 1     0.7659E+08    -0.1823E+05    -0.1306E+04     0.3727E+01
+ 1 2     0.4245E+08    -0.9703E+04    -0.1129E+04     0.0000E+00
+ 2 1     0.4245E+08    -0.9703E+04    -0.1129E+04     0.0000E+00
+ 2 2     0.6367E+08    -0.1565E+05    -0.3348E+03     0.5127E+01
+ Total average electrostatic energy:   -17.0351458449875     
+ VDW energy between peptide-group centers:   -10.2064531653452     
+ 
+ Electrostatic contacts before pruning: 
+  1  ASN   2  TYR   4  -1.06027
+  2  LEU   3  ILE   5  -1.59865
+  3  LEU   3  GLN   6  -0.54360
+  4  TYR   4  GLN   6  -2.10033
+  5  TYR   4  TRP   7  -0.84900
+  6  ILE   5  TRP   7  -1.85979
+  7  ILE   5  LEU   8  -0.53540
+  8  GLN   6  LEU   8  -1.48363
+  9  GLN   6  LYS   9  -0.61868
+ 10  TRP   7  LYS   9  -1.55464
+ 11  TRP   7  GLY  12  -0.37651
+ 12  LEU   8  ASP  10  -0.61626
+ 13  LEU   8  GLY  11  -0.40662
+ 
+ Electrostatic contacts after pruning: 
+  1  ASN   2  TYR   4  -1.06027
+  2  LEU   3  ILE   5  -1.59865
+  3  LEU   3  GLN   6  -0.54360
+  4  TYR   4  GLN   6  -2.10033
+  5  TYR   4  TRP   7  -0.84900
+  6  ILE   5  TRP   7  -1.85979
+  7  ILE   5  LEU   8  -0.53540
+  8  GLN   6  LEU   8  -1.48363
+  9  GLN   6  LYS   9  -0.61868
+ 10  TRP   7  LYS   9  -1.55464
+ 11  TRP   7  GLY  12  -0.37651
+ 12  LEU   8  ASP  10  -0.61626
+ 13  LEU   8  GLY  11  -0.40662
+Helix  1   2  10
+ UNRES seq:
+ helix            3          11
+ SC_move        1189  -4.13326717681629     
+PP contact map:
+  1  ASN   2  TYR   4
+  2  ASN   2  ILE   5
+  3  LEU   3  ILE   5
+  4  LEU   3  GLN   6
+  5  LEU   3  TRP   7
+  6  TYR   4  GLN   6
+  7  TYR   4  TRP   7
+  8  ILE   5  TRP   7
+  9  ILE   5  LEU   8
+ 10  GLN   6  LEU   8
+ 11  GLN   6  LYS   9
+ 12  TRP   7  LYS   9
+ 13  TRP   7  ASP  10
+ 14  TRP   7  GLY  11
+ 15  TRP   7  GLY  12
+ 16  LEU   8  ASP  10
+ 17  LEU   8  GLY  11
+ 18  LYS   9  GLY  11
+ 19  ASP  10  GLY  12
+ 20  GLY  11  PRO  13
+ 21  GLY  11  SER  14
+ 22  GLY  12  SER  14
+ 23  PRO  13  SER  15
+ 24  PRO  13  PRO  18
+ 25  SER  14  GLY  16
+ 26  SER  14  ARG  17
+ 27  SER  15  ARG  17
+ 28  PRO  18  PRO  20
+ Hairpins:
+Constants of electrostatic interaction energy expression.
+ 1 1     0.7659E+08    -0.1823E+05    -0.1306E+04     0.3727E+01
+ 1 2     0.4245E+08    -0.9703E+04    -0.1129E+04     0.0000E+00
+ 2 1     0.4245E+08    -0.9703E+04    -0.1129E+04     0.0000E+00
+ 2 2     0.6367E+08    -0.1565E+05    -0.3348E+03     0.5127E+01
+ Total average electrostatic energy:   -34.0939296423320     
+ VDW energy between peptide-group centers:    899.113237730561     
+ 
+ Electrostatic contacts before pruning: 
+  1  ASN   2  TYR   4 -10.17518
+  2  ASN   2  ILE   5  -1.20257
+  3  LEU   3  ILE   5 -10.90405
+  4  LEU   3  GLN   6  -1.04733
+  5  LEU   3  TRP   7  -0.51328
+  6  TYR   4  GLN   6  -1.11943
+  7  TYR   4  TRP   7  -0.47363
+  8  ILE   5  TRP   7  -1.27116
+  9  GLN   6  LEU   8  -0.57639
+ 10  TRP   7  LYS   9  -1.27183
+ 11  TRP   7  ASP  10  -0.33671
+ 12  LEU   8  ASP  10  -0.74960
+ 13  LEU   8  GLY  11  -0.44794
+ 14  GLY  12  SER  14  -0.51788
+ 
+ Electrostatic contacts after pruning: 
+  1  ASN   2  TYR   4 -10.17518
+  2  ASN   2  ILE   5  -1.20257
+  3  LEU   3  ILE   5 -10.90405
+  4  LEU   3  GLN   6  -1.04733
+  5  LEU   3  TRP   7  -0.51328
+  6  TYR   4  GLN   6  -1.11943
+  7  TYR   4  TRP   7  -0.47363
+  8  ILE   5  TRP   7  -1.27116
+  9  GLN   6  LEU   8  -0.57639
+ 10  TRP   7  LYS   9  -1.27183
+ 11  TRP   7  ASP  10  -0.33671
+ 12  LEU   8  ASP  10  -0.74960
+ 13  LEU   8  GLY  11  -0.44794
+ 14  GLY  12  SER  14  -0.51788
+Helix  1   1   7
+ UNRES seq:
+ helix            2           8
+
+Virtual-chain energies:
+
+EVDW=      6.783553E+02 WEIGHT=    1.352790D+00 (SC-SC)
+EVDW2=     2.098526E+04 WEIGHT=    1.593040D+00 (SC-p)
+EES=      -2.316959E+02 WEIGHT=    7.153400D-01 (p-p)
+EVDWPP=    3.102288E+03 WEIGHT=    1.137100D-01 (p-p VDW)
+ESTR=      6.779273E-27 WEIGHT=    1.000000D+00 (stretching)
+EBE=      -1.030472E+01 WEIGHT=    1.138730D+00 (bending)
+ESC=       5.035340E+32 WEIGHT=    1.625800D-01 (SC local)
+ETORS=     8.256991E+00 WEIGHT=    1.985990D+00 (torsional)
+ETORSD=    1.541091E+00 WEIGHT=    1.570690D+00 (double torsional)
+EHPB=      0.000000E+00 WEIGHT=    1.000000D+00 (SS bridges & dist. cnstr.)
+ECORR4=   -1.142431E+02 WEIGHT=    4.288700D-01 (multi-body)
+ECORR5=    0.000000E+00 WEIGHT=    0.000000D+00 (multi-body)
+ECORR6=    0.000000E+00 WEIGHT=    0.000000D+00 (multi-body)
+EELLO=  NaN             WEIGHT=    1.603600D-01 (electrostatic-local)
+ETURN3= NaN             WEIGHT=    1.687220D+00 (turns, 3rd order)
+ETURN4= NaN             WEIGHT=    6.623000D-01 (turns, 4th order)
+ETURN6=    0.000000E+00 WEIGHT=    0.000000D+00 (turns, 6th order)
+ESCCOR=    0.000000E+00 WEIGHT=    0.000000D+00 (backbone-rotamer corr)
+EDIHC=     0.000000E+00 (dihedral angle constraints)
+ESS=       0.000000E+00 (disulfide-bridge intrinsic energy)
+UCONST=     0.000000E+00 (Constraint energy)
+ETOT=      1.000000E+99 (total)
+
+Geometry of the virtual chain.
+  Res           d     Theta     Gamma       Dsc     Alpha      Beta 
+D     1     0.000     0.000     0.000     0.000     0.000     0.000
+ASN   2     3.800     0.000     0.000     1.684   166.403   -78.295
+LEU   3     3.800   118.535     0.000     1.939    98.410   -20.526
+TYR   4     3.800    91.262   -84.783     2.484   143.962   -14.485
+ILE   5     3.800     0.000    74.731     1.776   126.981  -107.717
+GLN   6     3.800    90.125    49.156     2.240   123.165  -131.319
+TRP   7     3.800    89.563    53.467     2.605   136.415   -30.509
+LEU   8     3.800    89.157    49.735     1.939   155.047  -119.048
+LYS   9     3.800    90.266    80.355     2.541   138.316  -137.964
+ASP  10     3.800    91.711    42.732     1.709   143.742  -133.222
+GLY  11     3.800    91.876    63.556     0.000   180.000   180.000
+GLY  12     3.800   115.894   -57.622     0.000   180.000   180.000
+PRO  13     3.800   120.076   -75.407     1.345   106.478   -96.392
+SER  14     3.800    92.479   -68.391     1.150   133.923   -99.369
+SER  15     3.800    94.169    65.963     1.150   114.383   -74.889
+GLY  16     3.800    93.692   138.023     0.000   180.000   180.000
+ARG  17     3.800    94.409   -73.682     3.020    95.051   -65.680
+PRO  18     3.800   130.488    58.633     1.345   120.711  -129.430
+PRO  19     3.800   117.860  -103.495     1.345   125.023  -135.544
+PRO  20     3.800   116.631  -108.533     1.345    97.647  -118.910
+SER  21     3.800    93.213  -137.715     1.150   119.341   -84.219
+D    22     3.800   120.091    73.011     0.000   180.000   180.000
+RMS deviation from the reference structure:   2.378
+ % of native contacts:  60.870
+ % of nonnative contacts:  39.130
+ contact order:   0.300
+SUMSL return code:  4
+# of energy evaluations:                 431
+# of energy evaluations/sec:        3335.758
+CG processor   0 is finishing work.
+ Total wall clock time  0.195312500000000       sec

diff --git a/examples/unres/MD/ff_gab/1L2Y_minim_GB.int b/examples/unres/MD/ff_gab/1L2Y_minim_GB.int
new file mode 100644 (file)
index 0000000..2f9bf8c
--- /dev/null
+++ b/examples/unres/MD/ff_gab/1L2Y_minim_GB.int
@@ -0,0 +1,13 @@
+    0     -78.629 0
+  118.4938   91.7167   90.0355   89.0402   90.4331   90.7695   90.5004   92.1025
+   91.3597  111.6806  113.6844   93.2625   93.9321  115.8645   94.3034  121.7562
+  117.8557  115.6233   93.8548  117.7927
+ -100.4277   63.6464   55.7934   45.2757   45.2407   50.3196   46.2887   65.7510
+  -71.6699  -58.6548  -78.1521   57.8486  137.4148  -84.3592   61.6350  -81.0853
+ -108.3267 -137.4501   46.0495
+  110.7016  141.2278  118.5494  146.6522  104.8935  138.7112  136.3949  134.1788
+  143.4752  180.0000  180.0000  129.7747  115.0099  124.8976  180.0000   90.1761
+  116.3394  141.9872   97.8769  144.1295
+  -85.6852  -49.5399  113.8683  -96.9727  -50.5662   59.2188 -145.4804 -136.3182
+ -124.4460  180.0000  180.0000 -154.0107  -77.0566 -144.2941  180.0000 -107.6874
+ -177.3783 -158.7148  -97.6530 -129.5456

diff --git a/examples/unres/MD/ff_gab/1L2Y_minim_GB.mol2 b/examples/unres/MD/ff_gab/1L2Y_minim_GB.mol2
new file mode 100644 (file)
index 0000000..e69de29

diff --git a/examples/unres/MD/ff_gab/1L2Y_minim_GB.pdb b/examples/unres/MD/ff_gab/1L2Y_minim_GB.pdb
new file mode 100644 (file)
index 0000000..e69de29

diff --git a/examples/unres/MD/ff_gab/1L2Y_minim_GB.stat b/examples/unres/MD/ff_gab/1L2Y_minim_GB.stat
new file mode 100644 (file)
index 0000000..e69de29

diff --git a/examples/unres/MD/ff_gab/1L2Y_minim_GB000.int b/examples/unres/MD/ff_gab/1L2Y_minim_GB000.int
new file mode 100644 (file)
index 0000000..e64ba47
--- /dev/null
+++ b/examples/unres/MD/ff_gab/1L2Y_minim_GB000.int
@@ -0,0 +1,13 @@
+    0************ 0
+  118.6889   91.7826    0.0000   90.6142   90.3584   90.5610   90.3893   91.8517
+   90.5697  105.6675   99.1585   92.4742   94.0291  115.0390   94.9803  125.0459
+  117.2452  121.1533   92.2810  116.7440
+ -149.5898   84.2508   45.4276   42.4792   45.5761   50.7277   44.6644   70.3941
+  -67.4870  -65.5727  -33.1437  101.4914  122.5310  -88.2079   63.7788  -83.6619
+ -109.8078 -149.2012  105.0201
+   66.0940  138.1088  123.9842  149.4976  118.6739  163.0952  145.2796  133.1762
+  133.9319  180.0000  180.0000  115.5719  113.5038  124.4199  180.0000  101.4361
+  121.6996  110.9385  105.3684  124.5323
+  -81.7460  -26.8931  108.1542  -90.9882 -118.9725   48.7228 -129.6748 -134.5051
+ -129.1828  180.0000  180.0000 -113.5817  -79.3178 -158.6472  180.0000 -102.1785
+ -130.5467 -109.3060 -111.8144 -120.7112

diff --git a/examples/unres/MD/ff_gab/1L2Y_minim_GB000.mol2 b/examples/unres/MD/ff_gab/1L2Y_minim_GB000.mol2
new file mode 100644 (file)
index 0000000..e69de29

diff --git a/examples/unres/MD/ff_gab/1L2Y_minim_GB000.pdb b/examples/unres/MD/ff_gab/1L2Y_minim_GB000.pdb
new file mode 100644 (file)
index 0000000..e69de29

diff --git a/examples/unres/MD/ff_gab/1L2Y_minim_GB000.stat b/examples/unres/MD/ff_gab/1L2Y_minim_GB000.stat
new file mode 100644 (file)
index 0000000..e69de29

diff --git a/examples/unres/MD/ff_gab/1L2Y_minim_LJ000.int b/examples/unres/MD/ff_gab/1L2Y_minim_LJ000.int
new file mode 100644 (file)
index 0000000..707ee24
--- /dev/null
+++ b/examples/unres/MD/ff_gab/1L2Y_minim_LJ000.int
@@ -0,0 +1,13 @@
+    0************ 0
+  118.5349   91.2615    0.0000   90.1249   89.5628   89.1570   90.2660   91.7107
+   91.8763  115.8941  120.0758   92.4795   94.1689   93.6918   94.4088  130.4883
+  117.8596  116.6312   93.2127  120.0906
+  -84.7829   74.7307   49.1557   53.4670   49.7352   80.3551   42.7322   63.5565
+  -57.6216  -75.4075  -68.3913   65.9628  138.0231  -73.6821   58.6330 -103.4954
+ -108.5326 -137.7154   73.0113
+  166.4029   98.4096  143.9619  126.9814  123.1648  136.4149  155.0468  138.3159
+  143.7423  180.0000  180.0000  106.4783  133.9230  114.3826  180.0000   95.0507
+  120.7111  125.0235   97.6472  119.3410
+  -78.2954  -20.5265  -14.4853 -107.7166 -131.3195  -30.5095 -119.0482 -137.9641
+ -133.2218  180.0000  180.0000  -96.3923  -99.3690  -74.8894  180.0000  -65.6796
+ -129.4301 -135.5437 -118.9101  -84.2187

diff --git a/examples/unres/MD/ff_gab/1L2Y_minim_LJ000.mol2 b/examples/unres/MD/ff_gab/1L2Y_minim_LJ000.mol2
new file mode 100644 (file)
index 0000000..e69de29

diff --git a/examples/unres/MD/ff_gab/1L2Y_minim_LJ000.pdb b/examples/unres/MD/ff_gab/1L2Y_minim_LJ000.pdb
new file mode 100644 (file)
index 0000000..e69de29

diff --git a/examples/unres/MD/ff_gab/1L2Y_minim_LJ000.stat b/examples/unres/MD/ff_gab/1L2Y_minim_LJ000.stat
new file mode 100644 (file)
index 0000000..e69de29

diff --git a/examples/unres/MD/ff_gab/fort.12 b/examples/unres/MD/ff_gab/fort.12
new file mode 100644 (file)
index 0000000..817ff02
--- /dev/null
+++ b/examples/unres/MD/ff_gab/fort.12
@@ -0,0 +1,8 @@
+DefPropRes 'helix1' 'num =   2..  9'
+DefPropRes 'helix' 'helix1'
+DefPropRes 'coil' '! (helix | sheet)'
+XMacStand ribbon.mac
+DefPropRes 'helix1' 'num =   3..  9'
+DefPropRes 'helix' 'helix1'
+DefPropRes 'coil' '! (helix | sheet)'
+XMacStand ribbon.mac

diff --git a/examples/unres/MD/ff_gab/start.mat b/examples/unres/MD/ff_gab/start.mat
new file mode 100755 (executable)
index 0000000..a1008ff
--- /dev/null
+++ b/examples/unres/MD/ff_gab/start.mat
@@ -0,0 +1,12 @@
+#PBS -N test
+#PBS -q dque
+#PBS -l nodes=1:ppn=1
+#PBS -l mem=2gb
+#PBS -l walltime=24:00:00
+
+setenv MPIRUN "/users/software/mpich-1.2.7p1_intel-10.1_em64_ssh/bin/mpirun "
+setenv NPROCS `cat $PBS_NODEFILE | wc -l`
+
+cd $PBS_O_WORKDIR
+$MPIRUN -machinefile $PBS_NODEFILE -np $NPROCS ./unres.csh
+

diff --git a/examples/unres/MD/ff_gab/test.e54333 b/examples/unres/MD/ff_gab/test.e54333
new file mode 100644 (file)
index 0000000..0a57c6d
--- /dev/null
+++ b/examples/unres/MD/ff_gab/test.e54333
@@ -0,0 +1 @@
+Bye Bye...

diff --git a/examples/unres/MD/ff_gab/test.e54334 b/examples/unres/MD/ff_gab/test.e54334
new file mode 100644 (file)
index 0000000..0a57c6d
--- /dev/null
+++ b/examples/unres/MD/ff_gab/test.e54334
@@ -0,0 +1 @@
+Bye Bye...

diff --git a/examples/unres/MD/ff_gab/test.o54333 b/examples/unres/MD/ff_gab/test.o54333
new file mode 100644 (file)
index 0000000..4a70449
--- /dev/null
+++ b/examples/unres/MD/ff_gab/test.o54333
@@ -0,0 +1,23 @@
+ Processor           0  out of           1  rank in CG_COMM           0 
+  size of CG_COMM           1  size of FG_COMM           1  rank in FG_COMM1
+           0  size of FG_COMM1           1
+Inside initialize MPI: node=            0  iseed(4)=            0           0         -46
+      -45086
+ indpdb=           0  pdbref= T
+ Call Read_Bridge.
+ ns=           0
+ Processor           0           0           0  ivec_start           1  ivec_end
+          21
+ after etotal
+ Calling OVERLAP_SC
+ SC_move        1189  -4.13326717681629     
+ Calling MINIMIZE.
+ SUMSL return code is           4  eval          430
+ # eval/s   3335.75757575758     
+ refstr= T
+CG processor   0 is finishing work.
+--------------------------------------
+Running PBS epilogue script
+
+Single processor job or ~/.nokill exist, no need to kill processes
+Done.

diff --git a/examples/unres/MD/ff_gab/test.o54334 b/examples/unres/MD/ff_gab/test.o54334
new file mode 100644 (file)
index 0000000..40667c9
--- /dev/null
+++ b/examples/unres/MD/ff_gab/test.o54334
@@ -0,0 +1,23 @@
+ Processor           0  out of           1  rank in CG_COMM           0 
+  size of CG_COMM           1  size of FG_COMM           1  rank in FG_COMM1
+           0  size of FG_COMM1           1
+Inside initialize MPI: node=            0  iseed(4)=            0           0         -46
+      -45086
+ indpdb=           0  pdbref= T
+ Call Read_Bridge.
+ ns=           0
+ Processor           0           0           0  ivec_start           1  ivec_end
+          21
+ after etotal
+ Calling OVERLAP_SC
+ SC_move        1190  -36.8538206659302     
+ Calling MINIMIZE.
+ SUMSL return code is           4  eval          552
+ # eval/s   3072.00000000000     
+ refstr= T
+CG processor   0 is finishing work.
+--------------------------------------
+Running PBS epilogue script
+
+Single processor job or ~/.nokill exist, no need to kill processes
+Done.

diff --git a/examples/unres/MD/ff_gab/unres.csh b/examples/unres/MD/ff_gab/unres.csh
new file mode 100755 (executable)
index 0000000..82b2f43
--- /dev/null
+++ b/examples/unres/MD/ff_gab/unres.csh
@@ -0,0 +1,31 @@
+#!/bin/csh -f
+# Script to run the program unresCSA on linux with MPICH/PBS (parallel version).
+#
+
+setenv OUT1FILE YES
+setenv FGPROCS 1
+setenv POT GB
+setenv PREFIX 1L2Y_minim
+
+set DD = /users/adam/UNRES/PARAM
+setenv UNRES_BIN /users/adam/unres/bin/unres/MD/unres_ifort_MPICH_GAB.exe
+#setenv UNRES_BIN /users/adam/unres/bin/unres/MD/unres_ifort_single_GAB.exe
+#---------------------------------
+setenv BONDPAR $DD/bond.parm 
+setenv THETPAR $DD/thetaml.5parm
+setenv ROTPAR $DD/scgauss.parm
+setenv TORPAR $DD/torsion_631Gdp.parm
+setenv TORDPAR $DD/torsion_double_631Gdp.parm
+setenv ELEPAR $DD/electr_631Gdp.parm
+setenv SIDEPAR ${DD}/sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16-10-8k
+#setenv SIDEPAR ${DD}/scinter_LJ.parm
+setenv FOURIER $DD/fourier_opt.parm.1igd_hc_iter3_3
+setenv SCPPAR $DD/scp.parm
+setenv SCCORPAR $DD/rotcorr_AM1.parm
+
+# Pattern database
+setenv PATTERN $DD/patterns.cart
+#--------------------------------------------
+
+$UNRES_BIN $*
+

diff --git a/examples/unres/MD/ff_gab/unres_single.sh b/examples/unres/MD/ff_gab/unres_single.sh
index 49c2cc2..0576f87 100755 (executable)
--- a/examples/unres/MD/ff_gab/unres_single.sh
+++ b/examples/unres/MD/ff_gab/unres_single.sh
@@ -2,9 +2,9 @@
 export POT=$1
 export PREFIX=$2
 #-----------------------------------------------------------------------------
 export POT=$1
 export PREFIX=$2
 #-----------------------------------------------------------------------------

-UNRES_BIN=../../../../bin/unres/MD/unres_gfortran_single.exe
+UNRES_BIN=../../../../bin/unres/MD/unres_ifort_single_GAB.exe

 #-----------------------------------------------------------------------------
 #-----------------------------------------------------------------------------

-DD=../../PARAM
+DD=../../../../PARAM

 export BONDPAR=$DD/bond.parm
 export THETPAR=$DD/thetaml.5parm
 export ROTPAR=$DD/scgauss.parm
 export BONDPAR=$DD/bond.parm
 export THETPAR=$DD/thetaml.5parm
 export ROTPAR=$DD/scgauss.parm

@@ -14,6 +14,7 @@ export ELEPAR=$DD/electr_631Gdp.parm
 export SIDEPAR=$DD/sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16-10-8k
 export FOURIER=$DD/fourier_opt.parm.1igd_hc_iter3_3
 export SCPPAR=$DD/scp.parm
 export SIDEPAR=$DD/sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16-10-8k
 export FOURIER=$DD/fourier_opt.parm.1igd_hc_iter3_3
 export SCPPAR=$DD/scp.parm

+export SCCORPAR=$DD/rotcorr_AM1.parm

 export PATTERN=$DD/patterns.cart
 #-----------------------------------------------------------------------------
 $UNRES_BIN
 export PATTERN=$DD/patterns.cart
 #-----------------------------------------------------------------------------
 $UNRES_BIN

diff --git a/source/wham/src/cinfo.f b/source/wham/src/cinfo.f
index 5ecce7a..97eabbe 100644 (file)
--- a/source/wham/src/cinfo.f
+++ b/source/wham/src/cinfo.f
@@ -1,10 +1,10 @@
 C DO NOT EDIT THIS FILE - IT HAS BEEN GENERATED BY COMPINFO.C
 C DO NOT EDIT THIS FILE - IT HAS BEEN GENERATED BY COMPINFO.C

-C 0 0 546
+C 0 0 565

       subroutine cinfo
       include 'COMMON.IOUNITS'
       write(iout,*)'++++ Compile info ++++'
       subroutine cinfo
       include 'COMMON.IOUNITS'
       write(iout,*)'++++ Compile info ++++'

-      write(iout,*)'Version 0.0 build 546'
-      write(iout,*)'compiled Sun May 20 07:28:19 2012'
+      write(iout,*)'Version 0.0 build 565'
+      write(iout,*)'compiled Tue May 29 04:48:26 2012'

       write(iout,*)'compiled by adam@matrix.chem.cornell.edu'
       write(iout,*)'OS name:    Linux '
       write(iout,*)'OS release: 2.6.34.9-69.fc13.x86_64 '
       write(iout,*)'compiled by adam@matrix.chem.cornell.edu'
       write(iout,*)'OS name:    Linux '
       write(iout,*)'OS release: 2.6.34.9-69.fc13.x86_64 '

diff --git a/source/wham/src/wham_calc1.F b/source/wham/src/wham_calc1.F
index 5783bd4..a6044cd 100644 (file)
--- a/source/wham/src/wham_calc1.F
+++ b/source/wham/src/wham_calc1.F
@@ -38,6 +38,7 @@ c      parameter (MaxHdim=200000)
       parameter (MaxPoint=MaxStr,
      & MaxPointProc=MaxStr_Proc)
       double precision finorm_max,potfac,entmin,entmax,expfac,vf
       parameter (MaxPoint=MaxStr,
      & MaxPointProc=MaxStr_Proc)
       double precision finorm_max,potfac,entmin,entmax,expfac,vf

+      double precision entfac_min,entfac_min_t

       parameter (finorm_max=1.0d0)
       integer islice
       integer i,ii,j,jj,k,kk,l,m,ind,iter,t,tmax,ient,ientmax,iln
       parameter (finorm_max=1.0d0)
       integer islice
       integer i,ii,j,jj,k,kk,l,m,ind,iter,t,tmax,ient,ientmax,iln

@@ -48,7 +49,8 @@ c      parameter (MaxHdim=200000)
       double precision energia(0:max_ene)
 #ifdef MPI
       integer tmax_t,upindE_p
       double precision energia(0:max_ene)
 #ifdef MPI
       integer tmax_t,upindE_p

-      double precision fi_p(MaxR,MaxT_h,Max_Parm)
+      double precision fi_p(MaxR,MaxT_h,Max_Parm),
+     &  fi_p_min(MaxR,MaxT_h,Max_Parm)

       double precision sumW_p(0:Max_GridT,Max_Parm),
      & sumE_p(0:Max_GridT,Max_Parm),sumEsq_p(0:Max_GridT,Max_Parm),
      & sumQ_p(MaxQ1,0:Max_GridT,Max_Parm),
       double precision sumW_p(0:Max_GridT,Max_Parm),
      & sumE_p(0:Max_GridT,Max_Parm),sumEsq_p(0:Max_GridT,Max_Parm),
      & sumQ_p(MaxQ1,0:Max_GridT,Max_Parm),

@@ -71,6 +73,7 @@ c      parameter (MaxHdim=200000)
      & sumEprim(0:NGridT,Max_Parm),sumEbis(0:NGridT,Max_Parm),betaT,
      & weight,econstr
       double precision fi(MaxR,maxT_h,Max_Parm),
      & sumEprim(0:NGridT,Max_Parm),sumEbis(0:NGridT,Max_Parm),betaT,
      & weight,econstr
       double precision fi(MaxR,maxT_h,Max_Parm),

+     & fi_min(MaxR,maxT_h,Max_Parm),

      & dd,dd1,dd2,hh,dmin,denom,finorm,avefi,pom,
      & hfin(0:MaxHdim,maxT_h),histE(0:maxindE),
      & hrmsrgy(0:MaxBinRgy,0:MaxBinRms,maxT_h),
      & dd,dd1,dd2,hh,dmin,denom,finorm,avefi,pom,
      & hfin(0:MaxHdim,maxT_h),histE(0:maxindE),
      & hrmsrgy(0:MaxBinRgy,0:MaxBinRms,maxT_h),

@@ -368,6 +371,7 @@ c              write (iout,*) 1.0d0/(beta_h(ib,iparm)*1.987D-3),ft
 ! Compute new free-energy values corresponding to the righ-hand side of the 
 ! equation and their derivatives.
         write (iout,*) "------------------------fi"
 ! Compute new free-energy values corresponding to the righ-hand side of the 
 ! equation and their derivatives.
         write (iout,*) "------------------------fi"

+        entfac_min=1.0d10

 #ifdef MPI
         do t=1,scount(me1)
 #else
 #ifdef MPI
         do t=1,scount(me1)
 #else

@@ -393,10 +397,67 @@ c              write (iout,*) 1.0d0/(beta_h(ib,iparm)*1.987D-3),ft
             enddo
           enddo
           entfac(t)=-dlog(denom)-vmax
             enddo
           enddo
           entfac(t)=-dlog(denom)-vmax

+          if (entfac(t).lt.entfac_min) entfac_min=entfac(t)

 #ifdef DEBUG
           write (iout,*) t,"vmax",vmax," denom",denom,"entfac",entfac(t)
 #endif
         enddo
 #ifdef DEBUG
           write (iout,*) t,"vmax",vmax," denom",denom,"entfac",entfac(t)
 #endif
         enddo

+c#ifdef MPI
+c        write (iout,*) "entfac_min before AllReduce",entfac_min
+c        call MPI_AllReduce(entfac_min,entfac_min_t,1,
+c     &         MPI_DOUBLE_PRECISION,MPI_MAX,WHAM_COMM,IERROR)
+c        entfac_min=entfac_min_t
+c        write (iout,*) "entfac_min after AllReduce",entfac_min
+c#endif
+c#ifdef MPI
+c        do t=1,scount(me)
+c          entfac(t)=entfac(t)-entfac_min
+c        enddo
+c#else
+c        do t=1,ntot(islice)
+c          entfac(t)=entfac(t)-entfac_min
+c        enddo
+c#endif
+        do iparm=1,nParmSet
+          do iib=1,nT_h(iparm)
+            do ii=1,nR(iib,iparm)
+#ifdef MPI
+              fi_p_min(ii,iib,iparm)=-1.0d10
+              do t=1,scount(me)
+                aux=v(t,ii,iib,iparm)+entfac(t)
+                if (aux.gt.fi_p_min(ii,iib,iparm))
+     &                                   fi_p_min(ii,iib,iparm)=aux
+              enddo
+#else
+              do t=1,ntot(islice)
+                aux=v(t,ii,iib,iparm)+entfac(t)
+                if (aux.gt.fi_min(ii,iib,iparm)) 
+     &                                     fi_min(ii,iib,iparm)=aux
+              enddo
+#endif
+            enddo ! ii
+          enddo ! iib
+        enddo ! iparm
+#ifdef MPI
+#ifdef DEBUG
+        write (iout,*) "fi_min before AllReduce"
+        do i=1,nParmSet
+          do j=1,nT_h(i)
+            write (iout,*) (i,j,k,fi_p_min(k,j,i),k=1,nR(j,i))
+          enddo
+        enddo
+#endif
+        call MPI_AllReduce(fi_p_min,fi_min,MaxR*MaxT_h*nParmSet,
+     &         MPI_DOUBLE_PRECISION,MPI_MAX,WHAM_COMM,IERROR)
+#ifdef DEBUG
+        write (iout,*) "fi_min after AllReduce"
+        do i=1,nParmSet
+          do j=1,nT_h(i)
+            write (iout,*) (i,j,k,fi_min(k,j,i),k=1,nR(j,i))
+          enddo
+        enddo
+#endif
+#endif

         do iparm=1,nParmSet
           do iib=1,nT_h(iparm)
             do ii=1,nR(iib,iparm)
         do iparm=1,nParmSet
           do iib=1,nT_h(iparm)
             do ii=1,nR(iib,iparm)

@@ -404,17 +465,18 @@ c              write (iout,*) 1.0d0/(beta_h(ib,iparm)*1.987D-3),ft
               fi_p(ii,iib,iparm)=0.0d0
               do t=1,scount(me)
                 fi_p(ii,iib,iparm)=fi_p(ii,iib,iparm)
               fi_p(ii,iib,iparm)=0.0d0
               do t=1,scount(me)
                 fi_p(ii,iib,iparm)=fi_p(ii,iib,iparm)

-     &            +dexp(v(t,ii,iib,iparm)+entfac(t))
+     &           +dexp(v(t,ii,iib,iparm)+entfac(t)-fi_min(ii,iib,iparm))

 #ifdef DEBUG
 #ifdef DEBUG

-              write (iout,'(4i5,3e15.5)') t,ii,iib,iparm,
-     &         v(t,ii,iib,iparm),entfac(t),fi_p(ii,iib,iparm)
+              write (iout,'(4i5,4e15.5)') t,ii,iib,iparm,
+     &         v(t,ii,iib,iparm),entfac(t),fi_min(ii,iib,iparm),
+     &         fi_p(ii,iib,iparm)

 #endif
               enddo
 #else
               fi(ii,iib,iparm)=0.0d0
               do t=1,ntot(islice)
                 fi(ii,iib,iparm)=fi(ii,iib,iparm)
 #endif
               enddo
 #else
               fi(ii,iib,iparm)=0.0d0
               do t=1,ntot(islice)
                 fi(ii,iib,iparm)=fi(ii,iib,iparm)

-     &            +dexp(v(t,ii,iib,iparm)+entfac(t))
+     &           +dexp(v(t,ii,iib,iparm)+entfac(t)-fi_min(ii,iib,iparm))

               enddo
 #endif
             enddo ! ii
               enddo
 #endif
             enddo ! ii

@@ -432,10 +494,12 @@ c              write (iout,*) 1.0d0/(beta_h(ib,iparm)*1.987D-3),ft
           enddo
         enddo
 #endif
           enddo
         enddo
 #endif

+#ifdef DEBUG

         write (iout,*) "REDUCE size",maxR,MaxT_h,nParmSet,
      &   maxR*MaxT_h*nParmSet
         write (iout,*) "MPI_COMM_WORLD",MPI_COMM_WORLD,
      &   " WHAM_COMM",WHAM_COMM
         write (iout,*) "REDUCE size",maxR,MaxT_h,nParmSet,
      &   maxR*MaxT_h*nParmSet
         write (iout,*) "MPI_COMM_WORLD",MPI_COMM_WORLD,
      &   " WHAM_COMM",WHAM_COMM

+#endif

         call MPI_Reduce(fi_p(1,1,1),fi(1,1,1),maxR*MaxT_h*nParmSet,
      &   MPI_DOUBLE_PRECISION,
      &   MPI_SUM,Master,WHAM_COMM,IERROR)
         call MPI_Reduce(fi_p(1,1,1),fi(1,1,1),maxR*MaxT_h*nParmSet,
      &   MPI_DOUBLE_PRECISION,
      &   MPI_SUM,Master,WHAM_COMM,IERROR)

@@ -455,7 +519,7 @@ c              write (iout,*) 1.0d0/(beta_h(ib,iparm)*1.987D-3),ft
         do iparm=1,nParmSet
           do ib=1,nT_h(iparm)
             do i=1,nR(ib,iparm)
         do iparm=1,nParmSet
           do ib=1,nT_h(iparm)
             do i=1,nR(ib,iparm)

-              fi(i,ib,iparm)=-dlog(fi(i,ib,iparm))
+              fi(i,ib,iparm)=-dlog(fi(i,ib,iparm))-fi_min(i,ib,iparm)

               avefi=avefi+fi(i,ib,iparm)
             enddo
           enddo
               avefi=avefi+fi(i,ib,iparm)
             enddo
           enddo

@@ -674,7 +738,6 @@ C Determine the minimum energes for all parameter sets and temperatures
       enddo
       write (iout,*) "potEmin_min",potEmin_min
 #endif
       enddo
       write (iout,*) "potEmin_min",potEmin_min
 #endif

-#undef DEBUG

 
 #ifdef MPI
       do t=0,tmax
 
 #ifdef MPI
       do t=0,tmax