.. _gmx sham:
gmx sham
========
Synopsis
--------
.. parsed-literal::
gmx sham [:strong:`-f` :emphasis:`[<.xvg>]`] [:strong:`-ge` :emphasis:`[<.xvg>]`] [:strong:`-ene` :emphasis:`[<.xvg>]`] [:strong:`-dist` :emphasis:`[<.xvg>]`]
[:strong:`-histo` :emphasis:`[<.xvg>]`] [:strong:`-bin` :emphasis:`[<.ndx>]`] [:strong:`-lp` :emphasis:`[<.xpm>]`]
[:strong:`-ls` :emphasis:`[<.xpm>]`] [:strong:`-lsh` :emphasis:`[<.xpm>]`] [:strong:`-lss` :emphasis:`[<.xpm>]`]
[:strong:`-ls3` :emphasis:`[<.pdb>]`] [:strong:`-g` :emphasis:`[<.log>]`] [:strong:`-[no]w`] [:strong:`-xvg` :emphasis:``]
[:strong:`-[no]time`] [:strong:`-b` :emphasis:``] [:strong:`-e` :emphasis:``] [:strong:`-ttol` :emphasis:``]
[:strong:`-n` :emphasis:``] [:strong:`-[no]d`] [:strong:`-[no]sham`] [:strong:`-tsham` :emphasis:``]
[:strong:`-pmin` :emphasis:``] [:strong:`-dim` :emphasis:``] [:strong:`-ngrid` :emphasis:``]
[:strong:`-xmin` :emphasis:``] [:strong:`-xmax` :emphasis:``] [:strong:`-pmax` :emphasis:``]
[:strong:`-gmax` :emphasis:``] [:strong:`-emin` :emphasis:``] [:strong:`-emax` :emphasis:``]
[:strong:`-nlevels` :emphasis:``]
Description
-----------
``gmx sham`` makes multi-dimensional free-energy, enthalpy and entropy plots.
``gmx sham`` reads one or more :ref:`.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 :ref:`.xvg `, :ref:`.xpm `, :ref:`.eps ` and :ref:`.pdb ` files
``-xvg`` (xmgrace)
xvg plot formatting: xmgrace, xmgr, none
``-[no]time`` (yes)
Expect a time in the input
``-b`` (-1)
First time to read from set
``-e`` (-1)
Last time to read from set
``-ttol`` (0)
Tolerance on time in appropriate units (usually ps)
``-n`` (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`` (298.15)
Temperature for single histogram analysis
``-pmin`` (0)
Minimum probability. Anything lower than this will be set to zero
``-dim`` (1 1 1)
Dimensions for distances, used for volume correction (max 3 values, dimensions > 3 will get the same value as the last)
``-ngrid`` (32 32 32)
Number of bins for energy landscapes (max 3 values, dimensions > 3 will get the same value as the last)
``-xmin`` (0 0 0)
Minimum for the axes in energy landscape (see above for > 3 dimensions)
``-xmax`` (1 1 1)
Maximum for the axes in energy landscape (see above for > 3 dimensions)
``-pmax`` (0)
Maximum probability in output, default is calculate
``-gmax`` (0)
Maximum free energy in output, default is calculate
``-emin`` (0)
Minimum enthalpy in output, default is calculate
``-emax`` (0)
Maximum enthalpy in output, default is calculate
``-nlevels`` (25)
Number of levels for energy landscape
.. only:: man
See also
--------
:manpage:`gmx(1)`
More information about |Gromacs| is available at .