g_sham1
Compute free energies or other histograms from histograms
Part of gmx-sham(1).
Usage
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
<int>]
[-
[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>]
Overview
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 r2 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
Releases
5 releases since Debian 4.0 (Etch); the text changed 4 times.