.. _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 .