---
name: "g_sham_d"
section: "1"
platform: "linux"
package: "gromacs-data"
version: "5.0.2-1"
release: "Debian 8 (Jessie)"
platforms: ["linux"]
url: "https://new.carta.tech/gmx-sham"
---

# g\_sham\_d(1)

Compute free energies or other histograms from histograms

Part of [gmx-sham(1)](/gmx-sham/1.md).

## 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 \[\<.log\>\]\] \[-nice \<int\>\]\
          \[-\[no\]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 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

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

## SEE ALSO

**[gromacs(7)](/gromacs/7.md)**

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