g_sham

Main Table of Contents

VERSION 4.6.3
Fri 5 Jul 2013


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 r^2 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

optionfilenametypedescription
-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

optiontypedefaultdescription
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]time bool yes 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]d bool no Use the derivative
-bw real 0.1 Binwidth for the distribution
-[no]sham bool yes 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


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