gmx sham

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