g_sham(1)
NAME
g_sham - read/write xmgr and xvgr data sets
SYNOPSIS
g_sham -f graph.xvg -ge gibbs.xvg -ene esham.xvg -dist ener.xvg -histo edist.xvg -bin bindex.ndx -ls gibbs.xpm -lsh enthalpy.xpm -lss entropy.xpm -map map.xpm -ls3 gibbs3.pdb -mdata mapdata.xvg -g shamlog.log -[no]h -nice int -[no]w -[no]xvgr -[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 -gmax real -nlevels int -mname string
DESCRIPTION
g_sham reads a number of xvg files and analyzes data sets. 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
seperated 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 has been biased by this free
energy.
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 free-energy for
this volume effect. The probability is normalized by r and r2 for a
dimension of 2 and 3 respectively. 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
- -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 Output, Opt.
- xvgr/xmgr file
- -g shamlog.log Output, Opt.
- Log file
OTHER OPTIONS
- -[no]h no
- Print help info and quit
- -nice int 19
- Set the nicelevel
- -[no]w no
- View output xvg, xpm, eps and pdb files
- -[no]xvgr yes
- Add specific codes (legends etc.) in the output xvg files for the
- xmgrace program
- -[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 sets seperated by &
- -[no]d no
- Use the derivative
- -bw real 0.1
- Binwidth for the distribution
- -[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)
- -gmax real 0
- Maximum level in output, 0 is calculate
- -nlevels int 25
- Number of levels for energy landscape from single histogram analysis
- -mname string
- Legend label for the custom landscape
SEE ALSO
- More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.