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GMX-SHAM(1)			     GROMACS			     GMX-SHAM(1)

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  his-
     tograms  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 sepa-
     rated 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 ensem-
     ble is not a Boltzmann ensemble, but needs to be biased by  this  free  en-
     ergy.  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 Ku-
     mar 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 parti-
     cles 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  am-
	    persand

     -[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 dimen-
	    sions)

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

     -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
     2026, GROMACS development team

2026.3				  Jun 25, 2026			     GMX-SHAM(1)
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