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g_sham - read/write xmgr and xvgr data setsVERSION4.0.1

g_sham-fgraph.xvg-gegibbs.xvg-eneesham.xvg-distener.xvg-histoedist.xvg-binbindex.ndx-lpprob.xpm-lsgibbs.xpm-lshenthalpy.xpm-lssentropy.xpm-mapmap.xpm-ls3gibbs3.pdb-mdatamapdata.xvg-gshamlog.log-[no]h-niceint-[no]w-[no]xvgr-[no]time-breal-ereal-ttolreal-nint-[no]d-bwreal-[no]sham-tshamreal-pminreal-dimvector-ngridvector-xminvector-xmaxvector-pmaxreal-gmaxreal-eminreal-emaxreal-nlevelsint-mnamestring

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 seperated by & (option-n), in this case only one y value is read from each line. All lines starting with and @ are skipped. Option-gecan 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-finput. Option-enecan 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-dimdimensions 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 r2 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.

-fgraph.xvgInputxvgr/xmgr file-gegibbs.xvgInput,Opt.xvgr/xmgr file-eneesham.xvgInput,Opt.xvgr/xmgr file-distener.xvgOutput,Opt.xvgr/xmgr file-histoedist.xvgOutput,Opt.xvgr/xmgr file-binbindex.ndxOutput,Opt.Index file-lpprob.xpmOutput,Opt.X PixMap compatible matrix file-lsgibbs.xpmOutput,Opt.X PixMap compatible matrix file-lshenthalpy.xpmOutput,Opt.X PixMap compatible matrix file-lssentropy.xpmOutput,Opt.X PixMap compatible matrix file-mapmap.xpmOutput,Opt.X PixMap compatible matrix file-ls3gibbs3.pdbOutput,Opt.Protein data bank file-mdatamapdata.xvgOutput,Opt.xvgr/xmgr file-gshamlog.logOutput,Opt.Log file

-[no]hnoPrint help info and quit-niceint19Set the nicelevel-[no]wnoView output xvg, xpm, eps and pdb files-[no]xvgryesAdd specific codes (legends etc.) in the output xvg files for the xmgrace program-[no]timeyesExpect a time in the input-breal-1First time to read from set-ereal-1Last time to read from set-ttolreal0Tolerance on time in appropriate units (usually ps)-nint1Read sets seperated by &-[no]dnoUse the derivative-bwreal0.1Binwidth for the distribution-[no]shamyesTurn off energy weighting even if energies are given-tshamreal298.15Temperature for single histogram analysis-pminreal0Minimum probability. Anything lower than this will be set to zero-dimvector111Dimensions for distances, used for volume correction (max 3 values, dimensions 3 will get the same value as the last)-ngridvector323232Number of bins for energy landscapes (max 3 values, dimensions 3 will get the same value as the last)-xminvector000Minimum for the axes in energy landscape (see above for 3 dimensions)-xmaxvector111Maximum for the axes in energy landscape (see above for 3 dimensions)-pmaxreal0Maximum probability in output, default is calculate-gmaxreal0Maximum free energy in output, default is calculate-eminreal0Minimum enthalpy in output, default is calculate-emaxreal0Maximum enthalpy in output, default is calculate-nlevelsint25Number of levels for energy landscape-mnamestringLegend label for the custom landscape

gromacs(7)More information aboutGROMACSis available at <http://www.gromacs.org/>. Thu 16 Oct 2008 g_sham(1)