g_sham(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c					 g_sham(1)

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	-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 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 vec-
       tors 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

       -mname string
	Legend label for the custom landscape

SEE ALSO

       gromacs(7)

       More information about GROMACS is available at <http://www.gromacs.org/>.

								  Mon 4 Apr 2011							 g_sham(1)