man g_sham (Commandes) - g_sham VERSION 3.3_beta_20050823
NAME
g_sham VERSION 3.3_beta_20050823
SYNOPSIS
g_sham -f graph.xvg -ge gibbs.xvg -ene esham.xvg -dist ener.xvg -histo edist.xvg -bin bindex.ndx -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 -gmax real -nlevels int -mname string
DESCRIPTION
g_sham reads a number of xvg files and analyzes data sets. 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 has been biased by this free energy.
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 free-energy for this volume effect. The probability is normalized by r and r2 for a dimension of 2 and 3 respectively. 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
-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]h no Print help info and quit
-nice int 19 Set the nicelevel
-[no]w no View output xvg, xpm, eps and pdb files
-[no]xvgr yes Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-[no]time 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 sets seperated by &
-[no]d no Use the derivative
-bw real 0.1 Binwidth for the distribution
-[no]sham 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)
-gmax real 0 Maximum level in output, 0 is calculate
-nlevels int 25 Number of levels for energy landscape from single histogram analysis
-mname string Legend label for the custom landscape