## g_sham

Main Table of Contents

VERSION 4.6
Sat 19 Jan 2013

### Description

`g_sham` makes multi-dimensional free-energy, enthalpy and entropy plots. `g_sham` reads one or more `.xvg` files and analyzes data sets. The basic purpose of `g_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 <it>y</it>-values may follow. Multiple sets can also be read when they are separated by & (option `-n`), in this case only one <it>y</it>-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.

### Files

option | filename | type | description
--- | --- | --- | ---
`-f` | `graph.xvg` | Input | xvgr/xmgr file
`-ge` | `gibbs.xvg` | Input, Opt. | xvgr/xmgr file
`-ene` | `esham.xvg` | Input, Opt. | xvgr/xmgr file
`-dist` | `ener.xvg` | Output, Opt. | xvgr/xmgr file
`-histo` | `edist.xvg` | Output, Opt. | xvgr/xmgr file
`-bin` | `bindex.ndx` | Output, Opt. | Index file
`-lp` | `prob.xpm` | Output, Opt. | X PixMap compatible matrix file
`-ls` | `gibbs.xpm` | Output, Opt. | X PixMap compatible matrix file
`-lsh` | `enthalpy.xpm` | Output, Opt. | X PixMap compatible matrix file
`-lss` | `entropy.xpm` | Output, Opt. | X PixMap compatible matrix file
`-map` | `map.xpm` | Output, Opt. | X PixMap compatible matrix file
`-ls3` | `gibbs3.pdb` | Output, Opt. | Protein data bank file
`-mdata` | `mapdata.xvg` | Input, Opt. | xvgr/xmgr file
`-g` | `shamlog.log` | Output, Opt. | Log file

### Other options

option | type | default | description
--- | --- | --- | ---
`-[no]h` | bool | `no` | Print help info and quit
`-[no]version` | bool | `no` | Print version info and quit
`-nice` | int | `19` | Set the nicelevel
`-[no]w` | bool | `no` | View output `.xvg`, `.xpm`, `.eps` and `.pdb` files
`-xvg` | enum | `xmgrace` | xvg plot formatting: `xmgrace`, `xmgr` or `none`
`-[no]time` | bool | `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` | bool | `no` | Use the derivative
`-bw` | real | `0.1` | Binwidth for the distribution
`-[no]sham` | bool | `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
`-mname` | string | `` | Legend label for the custom landscape

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