g_sham_d (1) - Linux Man Pages

g_sham_d: read/write xmgr and xvgr data sets

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/>.