g_sham

NAME

g_sham - read/write xmgr and xvgr data sets

VERSION 4.6.6

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

SEE ALSO

gromacs(7)

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