Provided by: gromacs-data_2019.3-2_all bug

NAME

       gmx-sham - Compute free energies or other histograms from histograms

SYNOPSIS

          gmx sham [-f [<.xvg>]] [-ge [<.xvg>]] [-ene [<.xvg>]] [-dist [<.xvg>]]
                   [-histo [<.xvg>]] [-bin [<.ndx>]] [-lp [<.xpm>]]
                   [-ls [<.xpm>]] [-lsh [<.xpm>]] [-lss [<.xpm>]]
                   [-ls3 [<.pdb>]] [-g [<.log>]] [-[no]w] [-xvg <enum>]
                   [-[no]time] [-b <real>] [-e <real>] [-ttol <real>]
                   [-n <int>] [-[no]d] [-[no]sham] [-tsham <real>]
                   [-pmin <real>] [-dim <vector>] [-ngrid <vector>]
                   [-xmin <vector>] [-xmax <vector>] [-pmax <real>]
                   [-gmax <real>] [-emin <real>] [-emax <real>]
                   [-nlevels <int>]

DESCRIPTION

       gmx  sham makes multi-dimensional free-energy, enthalpy and entropy plots.  gmx sham reads
       one or more .xvg files and analyzes data sets.  The basic purpose of gmx sham is  to  plot
       Gibbs  free  energy  landscapes  (option  -ls)  by  Bolzmann  inverting  multi-dimensional
       histograms (option -lp), but it can also make enthalpy (option -lsh) and  entropy  (option
       -lss)  plots.  The histograms can be made for any quantities the user supplies.  A line in
       the input file may start with a time (see option -time) and any  number  of  y-values  may
       follow.   Multiple sets can also be read when they are separated by & (option -n), in this
       case only one y-value is read from each line.   All  lines  starting  with  #  and  @  are
       skipped.

       Option  -ge  can  be  used  to supply a file with free energies when the ensemble is not a
       Boltzmann ensemble, but needs to be biased by this free energy. One free energy  value  is
       required for each (multi-dimensional) data point in the -f input.

       Option  -ene  can  be  used  to supply a file with energies.  These energies are used as a
       weighting function  in  the  single  histogram  analysis  method  by  Kumar  et  al.  When
       temperatures  are  supplied  (as  a  second column in the file), an experimental weighting
       scheme is applied. In addition the vales are used for making enthalpy and entropy plots.

       With option -dim, dimensions can be gives  for  distances.   When  a  distance  is  2-  or
       3-dimensional,  the  circumference  or  surface  sampled  by  two particles increases with
       increasing distance.  Depending on what one would like to show, one can choose to  correct
       the  histogram and free-energy for this volume effect.  The probability is normalized by r
       and r^2 for dimensions of 2 and 3, respectively.  A value of -1 is  used  to  indicate  an
       angle  in  degrees  between two vectors: a sin(angle) normalization will be applied.  Note
       that for angles between vectors the inner-product or cosine is  the  natural  quantity  to
       use, as it will produce bins of the same volume.

OPTIONS

       Options to specify input files:

       -f [<.xvg>] (graph.xvg)
              xvgr/xmgr file

       -ge [<.xvg>] (gibbs.xvg) (Optional)
              xvgr/xmgr file

       -ene [<.xvg>] (esham.xvg) (Optional)
              xvgr/xmgr file

       Options to specify output files:

       -dist [<.xvg>] (ener.xvg) (Optional)
              xvgr/xmgr file

       -histo [<.xvg>] (edist.xvg) (Optional)
              xvgr/xmgr file

       -bin [<.ndx>] (bindex.ndx) (Optional)
              Index file

       -lp [<.xpm>] (prob.xpm) (Optional)
              X PixMap compatible matrix file

       -ls [<.xpm>] (gibbs.xpm) (Optional)
              X PixMap compatible matrix file

       -lsh [<.xpm>] (enthalpy.xpm) (Optional)
              X PixMap compatible matrix file

       -lss [<.xpm>] (entropy.xpm) (Optional)
              X PixMap compatible matrix file

       -ls3 [<.pdb>] (gibbs3.pdb) (Optional)
              Protein data bank file

       -g [<.log>] (shamlog.log) (Optional)
              Log file

       Other options:

       -[no]w (no)
              View output .xvg, .xpm, .eps and .pdb files

       -xvg <enum> (xmgrace)
              xvg plot formatting: xmgrace, xmgr, none

       -[no]time (yes)
              Expect a time in the input

       -b <real> (-1)
              First time to read from set

       -e <real> (-1)
              Last time to read from set

       -ttol <real> (0)
              Tolerance on time in appropriate units (usually ps)

       -n <int> (1)
              Read this number of sets separated by lines containing only an ampersand

       -[no]d (no)
              Use the derivative

       -[no]sham (yes)
              Turn off energy weighting even if energies are given

       -tsham <real> (298.15)
              Temperature for single histogram analysis

       -pmin <real> (0)
              Minimum probability. Anything lower than this will be set to zero

       -dim <vector> (1 1 1)
              Dimensions  for distances, used for volume correction (max 3 values, dimensions > 3
              will get the same value as the last)

       -ngrid <vector> (32 32 32)
              Number of bins for energy landscapes (max 3 values, dimensions >  3  will  get  the
              same value as the last)

       -xmin <vector> (0 0 0)
              Minimum for the axes in energy landscape (see above for > 3 dimensions)

       -xmax <vector> (1 1 1)
              Maximum for the axes in energy landscape (see above for > 3 dimensions)

       -pmax <real> (0)
              Maximum probability in output, default is calculate

       -gmax <real> (0)
              Maximum free energy in output, default is calculate

       -emin <real> (0)
              Minimum enthalpy in output, default is calculate

       -emax <real> (0)
              Maximum enthalpy in output, default is calculate

       -nlevels <int> (25)
              Number of levels for energy landscape

SEE ALSO

       gmx(1)

       More information about GROMACS is available at <http://www.gromacs.org/>.

COPYRIGHT

       2019, GROMACS development team