---
name: "gmx-sham"
section: "1"
platform: "linux"
package: "gromacs-data"
version: "2025.2-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/gmx-sham"
---

# gmx-sham(1)

Compute free energies or other histograms from histograms

## NAME

gmx-sham - Compute free energies or other histograms from histograms

## 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>]] [-[no]w] [-xvg <enum>]
         [-[no]time] [-b <real>] [-e <real>] [-ttol <real>]
         [-n <int>] [-[no]d] [-[no]sham] [-tsham <real>]
         [-pmin <real>] [-dim <vector>] [-ngrid <vector>]
         [-xmin <vector>] [-xmax <vector>] [-pmax <real>]
         [-gmax <real>] [-emin <real>] [-emax <real>]
         [-nlevels <int>]
```

## DESCRIPTION

**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 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 inner-product or cosine is the natural quantity to use, as it will produce bins of the same volume.

## OPTIONS

Options to specify input files:

- **-f \[\<.xvg\>\] (graph.xvg)**

  xvgr/xmgr file

- **-ge \[\<.xvg\>\] (gibbs.xvg) (Optional)**

  xvgr/xmgr file

- **-ene \[\<.xvg\>\] (esham.xvg) (Optional)**

  xvgr/xmgr file

Options to specify output files:

- **-dist \[\<.xvg\>\] (ener.xvg) (Optional)**

  xvgr/xmgr file

- **-histo \[\<.xvg\>\] (edist.xvg) (Optional)**

  xvgr/xmgr file

- **-bin \[\<.ndx\>\] (bindex.ndx) (Optional)**

  Index file

- **-lp \[\<.xpm\>\] (prob.xpm) (Optional)**

  X PixMap compatible matrix file

- **-ls \[\<.xpm\>\] (gibbs.xpm) (Optional)**

  X PixMap compatible matrix file

- **-lsh \[\<.xpm\>\] (enthalpy.xpm) (Optional)**

  X PixMap compatible matrix file

- **-lss \[\<.xpm\>\] (entropy.xpm) (Optional)**

  X PixMap compatible matrix file

- **-ls3 \[\<.pdb\>\] (gibbs3.pdb) (Optional)**

  Protein data bank file

- **-g \[\<.log\>\] (shamlog.log) (Optional)**

  Log file

Other options:

- **-\[no\]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

## SEE ALSO

**[gmx(1)](/gmx/1.md)**

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

## COPYRIGHT

2025, GROMACS development team