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This is the command gmx-sham that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


gmx-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>]] [-[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>
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

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