Synopsis
gmx sham [f [<.xvg>]] [ge [<.xvg>]] [ene [<.xvg>]] [dist [<.xvg>]]
[histo [<.xvg>]] [bin [<.ndx>]] [lp [<.xpm>]] [ls [<.xpm>]]
[lsh [<.xpm>]] [lss [<.xpm>]] [ls3 [<.pdb>]] [g [<.log>]]
[nice ] [[no]w] [xvg ] [[no]time] [b ]
[e ] [ttol ] [n ] [[no]d] [[no]sham]
[tsham ] [pmin ] [dim ] [ngrid ]
[xmin ] [xmax ] [pmax ] [gmax ]
[emin ] [emax ] [nlevels ]
Description
gmx sham makes multidimensional freeenergy, enthalpy and entropy plots. gmx sham reads one or more .xvg files and analyzes data sets. The basic purpose of gmx sham is to plot Gibbs free energy landscapes (option ls) by Bolzmann inverting multidimensional 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 yvalues may follow. Multiple sets can also be read when they are separated by & (option n), in this case only one yvalue 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 (multidimensional) 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 3dimensional, 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 freeenergy 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 innerproduct or cosine is the natural quantity to use, as it will produce bins of the same volume.
Options
Options to specify input and output files:
 f [<.xvg>] (graph.xvg) (Input)

xvgr/xmgr file
 ge [<.xvg>] (gibbs.xvg) (Input, Optional)

xvgr/xmgr file
 ene [<.xvg>] (esham.xvg) (Input, Optional)

xvgr/xmgr file
 dist [<.xvg>] (ener.xvg) (Output, Optional)

xvgr/xmgr file
 histo [<.xvg>] (edist.xvg) (Output, Optional)

xvgr/xmgr file
 bin [<.ndx>] (bindex.ndx) (Output, Optional)

Index file
 lp [<.xpm>] (prob.xpm) (Output, Optional)

X PixMap compatible matrix file
 ls [<.xpm>] (gibbs.xpm) (Output, Optional)

X PixMap compatible matrix file
 lsh [<.xpm>] (enthalpy.xpm) (Output, Optional)

X PixMap compatible matrix file
 lss [<.xpm>] (entropy.xpm) (Output, Optional)

X PixMap compatible matrix file
 ls3 [<.pdb>] (gibbs3.pdb) (Output, Optional)

Protein data bank file
 g [<.log>] (shamlog.log) (Output, Optional)

Log file
Other options:
 nice <int> (19)

Set the nicelevel
 [no]w (no)

View output .xvg, .xpm, .eps and .pdb files
 xvg <enum> (xmgrace)

xvg plot formatting: xmgrace, xmgr, none
 [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 this number of sets separated by lines containing only an ampersand
 [no]d (no)

Use the derivative
 [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)
 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