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:

Options to specify output files:

Other options:

SEE ALSO¶

gmx(1)

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

COPYRIGHT¶

2022, GROMACS development team