# gmx sham¶

## 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> (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