**gmx sham** makes multi-dimensional free-energy, 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 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 vectors the inner-product or cosine is the natural quantity to use, as it will produce bins of the same volume.

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