gmx-sham(1) GROMACS Manual gmx-sham(1)NAMEgmx-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>]] [-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>]
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-dimen‐
sional) 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 col‐
umn in the file), an experimental weighting scheme is applied. In addi‐
tion the vales are used for making enthalpy and entropy plots.
With option -dim, dimensions can be gives for distances. When a dis‐
tance 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) nor‐
malization will be applied. Note that for angles between vectors the
inner-product or cosine is the natural quantity to use, as it will pro‐
duce 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 dimen‐
sions)
-xmax <vector> (1 1 1)
Maximum for the axes in energy landscape (see above for 3 dimen‐
sions)
-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 ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-sham(1)
