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

       2025, GROMACS development team

2025.0                                            Feb 10, 2025                                       GMX-SHAM(1)

gmxsham  makes  multi-dimensional  free-energy, enthalpy and entropy plots.  gmxsham reads one or more
       .xvg files and analyzes data sets.  The basic purpose of gmxsham 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.

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

       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>(111)
              Dimensions  for  distances,  used for volume correction (max 3 values, dimensions > 3 will get the
              same value as the last)

       -ngrid<vector>(323232)
              Number of bins for energy landscapes (max 3 values, dimensions > 3 will get the same value as  the
              last)

       -xmin<vector>(000)
              Minimum for the axes in energy landscape (see above for > 3 dimensions)

       -xmax<vector>(111)
              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

gmx(1)

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

          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>]