.TH g_sham 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME g_sham - read/write xmgr and xvgr data sets .B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3g_sham\fP .BI "\-f" " graph.xvg " .BI "\-ge" " gibbs.xvg " .BI "\-ene" " esham.xvg " .BI "\-dist" " ener.xvg " .BI "\-histo" " edist.xvg " .BI "\-bin" " bindex.ndx " .BI "\-lp" " prob.xpm " .BI "\-ls" " gibbs.xpm " .BI "\-lsh" " enthalpy.xpm " .BI "\-lss" " entropy.xpm " .BI "\-map" " map.xpm " .BI "\-ls3" " gibbs3.pdb " .BI "\-mdata" " mapdata.xvg " .BI "\-g" " shamlog.log " .BI "\-[no]h" "" .BI "\-[no]version" "" .BI "\-nice" " int " .BI "\-[no]w" "" .BI "\-xvg" " enum " .BI "\-[no]time" "" .BI "\-b" " real " .BI "\-e" " real " .BI "\-ttol" " real " .BI "\-n" " int " .BI "\-[no]d" "" .BI "\-bw" " real " .BI "\-[no]sham" "" .BI "\-tsham" " real " .BI "\-pmin" " real " .BI "\-dim" " vector " .BI "\-ngrid" " vector " .BI "\-xmin" " vector " .BI "\-xmax" " vector " .BI "\-pmax" " real " .BI "\-gmax" " real " .BI "\-emin" " real " .BI "\-emax" " real " .BI "\-nlevels" " int " .BI "\-mname" " string " .SH DESCRIPTION \&\fB g_sham\fR makes multi\-dimensional free\-energy, enthalpy and entropy plots. \&\fB g_sham\fR reads one or more \fB .xvg\fR files and analyzes data sets. \&The basic purpose of \fB g_sham\fR is to plot Gibbs free energy landscapes \&(option \fB \-ls\fR) \&by Bolzmann inverting multi\-dimensional histograms (option \fB \-lp\fR), \&but it can also \&make enthalpy (option \fB \-lsh\fR) and entropy (option \fB \-lss\fR) \&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\fR) and any number of \fI y\fR\-values may follow. \&Multiple sets can also be \&read when they are separated by & (option \fB \-n\fR), \&in this case only one \fI y\fR\-value is read from each line. \&All lines starting with and @ are skipped. \& \&Option \fB \-ge\fR 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\fR input. \& \&Option \fB \-ene\fR 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 \fB \-dim\fR, 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 r2 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. \&\fB Note\fR 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 FILES .BI "\-f" " graph.xvg" .B Input xvgr/xmgr file .BI "\-ge" " gibbs.xvg" .B Input, Opt. xvgr/xmgr file .BI "\-ene" " esham.xvg" .B Input, Opt. xvgr/xmgr file .BI "\-dist" " ener.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-histo" " edist.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-bin" " bindex.ndx" .B Output, Opt. Index file .BI "\-lp" " prob.xpm" .B Output, Opt. X PixMap compatible matrix file .BI "\-ls" " gibbs.xpm" .B Output, Opt. X PixMap compatible matrix file .BI "\-lsh" " enthalpy.xpm" .B Output, Opt. X PixMap compatible matrix file .BI "\-lss" " entropy.xpm" .B Output, Opt. X PixMap compatible matrix file .BI "\-map" " map.xpm" .B Output, Opt. X PixMap compatible matrix file .BI "\-ls3" " gibbs3.pdb" .B Output, Opt. Protein data bank file .BI "\-mdata" " mapdata.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-g" " shamlog.log" .B Output, Opt. Log file .SH OTHER OPTIONS .BI "\-[no]h" "no " Print help info and quit .BI "\-[no]version" "no " Print version info and quit .BI "\-nice" " int" " 19" Set the nicelevel .BI "\-[no]w" "no " View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR .BI "\-[no]time" "yes " Expect a time in the input .BI "\-b" " real" " \-1 " First time to read from set .BI "\-e" " real" " \-1 " Last time to read from set .BI "\-ttol" " real" " 0 " Tolerance on time in appropriate units (usually ps) .BI "\-n" " int" " 1" Read sets separated by & .BI "\-[no]d" "no " Use the derivative .BI "\-bw" " real" " 0.1 " Binwidth for the distribution .BI "\-[no]sham" "yes " Turn off energy weighting even if energies are given .BI "\-tsham" " real" " 298.15" Temperature for single histogram analysis .BI "\-pmin" " real" " 0 " Minimum probability. Anything lower than this will be set to zero .BI "\-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) .BI "\-ngrid" " vector" " 32 32 32" Number of bins for energy landscapes (max 3 values, dimensions 3 will get the same value as the last) .BI "\-xmin" " vector" " 0 0 0" Minimum for the axes in energy landscape (see above for 3 dimensions) .BI "\-xmax" " vector" " 1 1 1" Maximum for the axes in energy landscape (see above for 3 dimensions) .BI "\-pmax" " real" " 0 " Maximum probability in output, default is calculate .BI "\-gmax" " real" " 0 " Maximum free energy in output, default is calculate .BI "\-emin" " real" " 0 " Minimum enthalpy in output, default is calculate .BI "\-emax" " real" " 0 " Maximum enthalpy in output, default is calculate .BI "\-nlevels" " int" " 25" Number of levels for energy landscape .BI "\-mname" " string" " " Legend label for the custom landscape .SH SEE ALSO .BR gromacs(7) More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.