g_sham(1) - Linux man page

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 -histoedist.xvg -bin bindex.ndx -lp prob.xpm -ls gibbs.xpm -lsh enthalpy.xpm -lssentropy.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 -ttolreal -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