NAME
g_sham - read/write xmgr and xvgr data sets
VERSION 4.0.1
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 -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 -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. g_sham
basic purpose is plotting 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 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 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 due to Kumar et. al. When also 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 a dimension 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 Output, Opt.
xvgr/xmgr file
-g shamlog.log Output, Opt.
Log file
OTHER OPTIONS
-[no]hno
Print help info and quit
-nice int 19
Set the nicelevel
-[no]wno
View output xvg, xpm, eps and pdb files
-[no]xvgryes
Add specific codes (legends etc.) in the output xvg files for the
xmgrace program
-[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 sets seperated by &
-[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
SEE ALSO
gromacs(7)
More information about GROMACS is available at
<http://www.gromacs.org/>.
Thu 16 Oct 2008 g_sham(1)