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 ] [-[no]w] [-xvg ] [-[no]time] [-b ]
[-e ] [-ttol ] [-n ] [-[no]d] [-[no]sham]
[-tsham ] [-pmin ] [-dim ] [-ngrid ]
[-xmin ] [-xmax ] [-pmax ] [-gmax ]
[-emin ] [-emax ] [-nlevels ]
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 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
