Ubuntu Manpage: g_sham - read/write xmgr and xvgr data sets

Provided by: gromacs-data_4.6.5-1build1_all

NAME

       g_sham - read/write xmgr and xvgr data sets

       VERSION 4.6.5

SYNOPSIS

       g_sham  -f  graph.xvg  -ge  gibbs.xvg  -ene esham.xvg -dist ener.xvg -histo edist.xvg -bin bindex.ndx -lp
       prob.xpm -ls gibbs.xpm -lsh enthalpy.xpm -lss entropy.xpm -map map.xpm -ls3 gibbs3.pdb -mdata mapdata.xvg
       -g shamlog.log -[no]h -[no]version -nice int -[no]w -xvg enum -[no]time -b real -e real -ttol real -n int
       -[no]d -bw real -[no]sham -tsham real -pmin real -dim vector -ngrid  vector  -xmin  vector  -xmax  vector
       -pmax real -gmax real -emin real -emax real -nlevels int -mname string

DESCRIPTION

g_sham makes multi-dimensional free-energy, enthalpy and entropy plots. g_sham reads one or more .xvg
files and analyzes data sets. The basic purpose of g_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 r2 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.

FILES

       -f graph.xvg Input
        xvgr/xmgr file

       -ge gibbs.xvg Input, Opt.
        xvgr/xmgr file

       -ene esham.xvg Input, Opt.
        xvgr/xmgr file

       -dist ener.xvg Output, Opt.
        xvgr/xmgr file

       -histo edist.xvg Output, Opt.
        xvgr/xmgr file

       -bin bindex.ndx Output, Opt.
        Index file

       -lp prob.xpm Output, Opt.
        X PixMap compatible matrix file

       -ls gibbs.xpm Output, Opt.
        X PixMap compatible matrix file

       -lsh enthalpy.xpm Output, Opt.
        X PixMap compatible matrix file

       -lss entropy.xpm Output, Opt.
        X PixMap compatible matrix file

       -map map.xpm Output, Opt.
        X PixMap compatible matrix file

       -ls3 gibbs3.pdb Output, Opt.
        Protein data bank file

       -mdata mapdata.xvg Input, Opt.
        xvgr/xmgr file

       -g shamlog.log Output, Opt.
        Log file

OTHER OPTIONS

       -[no]hno
        Print help info and quit

       -[no]versionno
        Print version info and quit

       -nice int 19
        Set the nicelevel

       -[no]wno
        View output  .xvg,  .xpm,  .eps and  .pdb files

       -xvg enum xmgrace
        xvg plot formatting:  xmgrace,  xmgr or  none

       -[no]timeyes
        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]dno
        Use the derivative

       -bw real 0.1
        Binwidth for the distribution

       -[no]shamyes
        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

       -mname string
        Legend label for the custom landscape

NAME

SYNOPSIS

DESCRIPTION

FILES

OTHER OPTIONS

SEE ALSO