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g_shamMain Table of Contents |
VERSION 4.5
Thu 26 Aug 2010
| VERSION 4.5 |
g_sham makes multi-dimensional free-energy, enthalpy and entropy plots. g_sham reads one or more xvg files and analyzes data sets. g_sham basic purpose is plotting 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 due to Kumar et. al. When also 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 a dimension 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.
| 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 | Output, Opt. | xvgr/xmgr file |
| -g | shamlog.log | Output, Opt. | Log file |
| option | type | default | description |
|---|---|---|---|
| -[no]h | gmx_bool | no | Print help info and quit |
| -[no]version | gmx_bool | no | Print version info and quit |
| -nice | int | 19 | Set the nicelevel |
| -[no]w | gmx_bool | no | View output xvg, xpm, eps and pdb files |
| -xvg | enum | xmgrace | xvg plot formatting: xmgrace, xmgr or none |
| -[no]time | gmx_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 # sets separated by & |
| -[no]d | gmx_bool | no | Use the derivative |
| -bw | real | 0.1 | Binwidth for the distribution |
| -[no]sham | gmx_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 |