table of contents
g_sham(1) | GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c | g_sham(1) |
NAME¶
g_sham - read/write xmgr and xvgr data setsSYNOPSIS¶
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 stringDESCRIPTION¶
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.FILES¶
-f graph.xvg Inputxvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
Index file
X PixMap compatible matrix file
X PixMap compatible matrix file
X PixMap compatible matrix file
X PixMap compatible matrix file
X PixMap compatible matrix file
Protein data bank file
xvgr/xmgr file
Log file
OTHER OPTIONS¶
-[no]hnoPrint help info and quit
Print version info and quit
Set the nicelevel
View output .xvg, .xpm, .eps and .pdb files
xvg plot formatting: xmgrace, xmgr or none
Expect a time in the input
First time to read from set
Last time to read from set
Tolerance on time in appropriate units (usually ps)
Read sets separated by &
Use the derivative
Binwidth for the distribution
Turn off energy weighting even if energies are given
Temperature for single histogram analysis
Minimum probability. Anything lower than this will be set to zero
Dimensions for distances, used for volume correction (max 3 values, dimensions 3 will get the same value as the last)
Number of bins for energy landscapes (max 3 values, dimensions 3 will get the same value as the last)
Minimum for the axes in energy landscape (see above for 3 dimensions)
Maximum for the axes in energy landscape (see above for 3 dimensions)
Maximum probability in output, default is calculate
Maximum free energy in output, default is calculate
Minimum enthalpy in output, default is calculate
Maximum enthalpy in output, default is calculate
Number of levels for energy landscape
Legend label for the custom landscape
SEE ALSO¶
gromacs(7)Mon 4 Apr 2011 |