NAME¶

g_sham - read/write xmgr and xvgr data sets VERSION 4.5.4-dev-20110404-bc5695c

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 Output, 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 sets separated 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/>.