DOKK / manpages / debian 12 / gromacs-data / gmx-sham.1.en
GMX-SHAM(1) GROMACS GMX-SHAM(1)

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

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>]


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 to specify input files:


Options to specify output files:


Other options:

-[no]w (no)
View output .xvg, .xpm, .eps and .pdb files
xvg plot formatting: xmgrace, xmgr, none
-[no]time (yes)
Expect a time in the input
First time to read from set
Last time to read from set
Tolerance on time in appropriate units (usually ps)
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
Temperature for single histogram analysis
Minimum probability. Anything lower than this will be set to zero
Dimensions for distances, used for volume correction (max 3 values, dimensions > 3 will get the same value as the last)
Number of bins for energy landscapes (max 3 values, dimensions > 3 will get the same value as the last)
Minimum for the axes in energy landscape (see above for > 3 dimensions)
Maximum for the axes in energy landscape (see above for > 3 dimensions)
Maximum probability in output, default is calculate
Maximum free energy in output, default is calculate
Minimum enthalpy in output, default is calculate
Maximum enthalpy in output, default is calculate
Number of levels for energy landscape

gmx(1)

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

2023, GROMACS development team

February 3, 2023 2022.5