Provided by: gromacs-data_2020.1-1_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/>.


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       2020, GROMACS development team