.\" Man page generated from reStructuredText. . .TH "GMX-SHAM" "1" "Mar 29, 2021" "2020.6-Debian-2020.6-2" "GROMACS" .SH NAME gmx-sham \- Compute free energies or other histograms from histograms . .nr rst2man-indent-level 0 . .de1 rstReportMargin \\$1 \\n[an-margin] level \\n[rst2man-indent-level] level margin: \\n[rst2man-indent\\n[rst2man-indent-level]] - \\n[rst2man-indent0] \\n[rst2man-indent1] \\n[rst2man-indent2] .. .de1 INDENT .\" .rstReportMargin pre: . RS \\$1 . nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin] . nr rst2man-indent-level +1 .\" .rstReportMargin post: .. .de UNINDENT . RE .\" indent \\n[an-margin] .\" old: \\n[rst2man-indent\\n[rst2man-indent-level]] .nr rst2man-indent-level -1 .\" new: \\n[rst2man-indent\\n[rst2man-indent-level]] .in \\n[rst2man-indent\\n[rst2man-indent-level]]u .. .SH SYNOPSIS .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C gmx sham [\fB\-f\fP \fI[<.xvg>]\fP] [\fB\-ge\fP \fI[<.xvg>]\fP] [\fB\-ene\fP \fI[<.xvg>]\fP] [\fB\-dist\fP \fI[<.xvg>]\fP] [\fB\-histo\fP \fI[<.xvg>]\fP] [\fB\-bin\fP \fI[<.ndx>]\fP] [\fB\-lp\fP \fI[<.xpm>]\fP] [\fB\-ls\fP \fI[<.xpm>]\fP] [\fB\-lsh\fP \fI[<.xpm>]\fP] [\fB\-lss\fP \fI[<.xpm>]\fP] [\fB\-ls3\fP \fI[<.pdb>]\fP] [\fB\-g\fP \fI[<.log>]\fP] [\fB\-[no]w\fP] [\fB\-xvg\fP \fI\fP] [\fB\-[no]time\fP] [\fB\-b\fP \fI\fP] [\fB\-e\fP \fI\fP] [\fB\-ttol\fP \fI\fP] [\fB\-n\fP \fI\fP] [\fB\-[no]d\fP] [\fB\-[no]sham\fP] [\fB\-tsham\fP \fI\fP] [\fB\-pmin\fP \fI\fP] [\fB\-dim\fP \fI\fP] [\fB\-ngrid\fP \fI\fP] [\fB\-xmin\fP \fI\fP] [\fB\-xmax\fP \fI\fP] [\fB\-pmax\fP \fI\fP] [\fB\-gmax\fP \fI\fP] [\fB\-emin\fP \fI\fP] [\fB\-emax\fP \fI\fP] [\fB\-nlevels\fP \fI\fP] .ft P .fi .UNINDENT .UNINDENT .SH DESCRIPTION .sp \fBgmx sham\fP makes multi\-dimensional free\-energy, enthalpy and entropy plots. \fBgmx sham\fP reads one or more \&.xvg files and analyzes data sets. The basic purpose of \fBgmx sham\fP is to plot Gibbs free energy landscapes (option \fB\-ls\fP) by Bolzmann inverting multi\-dimensional histograms (option \fB\-lp\fP), but it can also make enthalpy (option \fB\-lsh\fP) and entropy (option \fB\-lss\fP) 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 \fB\-time\fP) and any number of \fIy\fP\-values may follow. Multiple sets can also be read when they are separated by & (option \fB\-n\fP), in this case only one \fIy\fP\-value is read from each line. All lines starting with # and @ are skipped. .sp Option \fB\-ge\fP 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 \fB\-f\fP input. .sp Option \fB\-ene\fP 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. .sp With option \fB\-dim\fP, 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. \fBNote\fP 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. .SH OPTIONS .sp Options to specify input files: .INDENT 0.0 .TP .B \fB\-f\fP [<.xvg>] (graph.xvg) xvgr/xmgr file .TP .B \fB\-ge\fP [<.xvg>] (gibbs.xvg) (Optional) xvgr/xmgr file .TP .B \fB\-ene\fP [<.xvg>] (esham.xvg) (Optional) xvgr/xmgr file .UNINDENT .sp Options to specify output files: .INDENT 0.0 .TP .B \fB\-dist\fP [<.xvg>] (ener.xvg) (Optional) xvgr/xmgr file .TP .B \fB\-histo\fP [<.xvg>] (edist.xvg) (Optional) xvgr/xmgr file .TP .B \fB\-bin\fP [<.ndx>] (bindex.ndx) (Optional) Index file .TP .B \fB\-lp\fP [<.xpm>] (prob.xpm) (Optional) X PixMap compatible matrix file .TP .B \fB\-ls\fP [<.xpm>] (gibbs.xpm) (Optional) X PixMap compatible matrix file .TP .B \fB\-lsh\fP [<.xpm>] (enthalpy.xpm) (Optional) X PixMap compatible matrix file .TP .B \fB\-lss\fP [<.xpm>] (entropy.xpm) (Optional) X PixMap compatible matrix file .TP .B \fB\-ls3\fP [<.pdb>] (gibbs3.pdb) (Optional) Protein data bank file .TP .B \fB\-g\fP [<.log>] (shamlog.log) (Optional) Log file .UNINDENT .sp Other options: .INDENT 0.0 .TP .B \fB\-[no]w\fP (no) View output \&.xvg, \&.xpm, \&.eps and \&.pdb files .TP .B \fB\-xvg\fP (xmgrace) xvg plot formatting: xmgrace, xmgr, none .TP .B \fB\-[no]time\fP (yes) Expect a time in the input .TP .B \fB\-b\fP (\-1) First time to read from set .TP .B \fB\-e\fP (\-1) Last time to read from set .TP .B \fB\-ttol\fP (0) Tolerance on time in appropriate units (usually ps) .TP .B \fB\-n\fP (1) Read this number of sets separated by lines containing only an ampersand .TP .B \fB\-[no]d\fP (no) Use the derivative .TP .B \fB\-[no]sham\fP (yes) Turn off energy weighting even if energies are given .TP .B \fB\-tsham\fP (298.15) Temperature for single histogram analysis .TP .B \fB\-pmin\fP (0) Minimum probability. Anything lower than this will be set to zero .TP .B \fB\-dim\fP (1 1 1) Dimensions for distances, used for volume correction (max 3 values, dimensions > 3 will get the same value as the last) .TP .B \fB\-ngrid\fP (32 32 32) Number of bins for energy landscapes (max 3 values, dimensions > 3 will get the same value as the last) .TP .B \fB\-xmin\fP (0 0 0) Minimum for the axes in energy landscape (see above for > 3 dimensions) .TP .B \fB\-xmax\fP (1 1 1) Maximum for the axes in energy landscape (see above for > 3 dimensions) .TP .B \fB\-pmax\fP (0) Maximum probability in output, default is calculate .TP .B \fB\-gmax\fP (0) Maximum free energy in output, default is calculate .TP .B \fB\-emin\fP (0) Minimum enthalpy in output, default is calculate .TP .B \fB\-emax\fP (0) Maximum enthalpy in output, default is calculate .TP .B \fB\-nlevels\fP (25) Number of levels for energy landscape .UNINDENT .SH SEE ALSO .sp \fBgmx(1)\fP .sp More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>. .SH COPYRIGHT 2021, GROMACS development team .\" Generated by docutils manpage writer. .