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| GMX-SHAM(1) | GROMACS | GMX-SHAM(1) |
NAME
gmx-sham - Compute free energies or other histograms from histogramsSYNOPSIS
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)More information about GROMACS is available at <http://www.gromacs.org/>.
COPYRIGHT
2022, GROMACS development team| January 14, 2022 | 2021.5 |
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