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g_sham

NAME

g_sham − read/write xmgr and xvgr data sets

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

SEE ALSO

gromacs(7)

More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.

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