1 .TH g_sham 1 "Fri 19 Apr 2013" "" "GROMACS suite, VERSION 4.5.7"
3 g_sham - read/write xmgr and xvgr data sets
8 .BI "\-f" " graph.xvg "
9 .BI "\-ge" " gibbs.xvg "
10 .BI "\-ene" " esham.xvg "
11 .BI "\-dist" " ener.xvg "
12 .BI "\-histo" " edist.xvg "
13 .BI "\-bin" " bindex.ndx "
14 .BI "\-lp" " prob.xpm "
15 .BI "\-ls" " gibbs.xpm "
16 .BI "\-lsh" " enthalpy.xpm "
17 .BI "\-lss" " entropy.xpm "
18 .BI "\-map" " map.xpm "
19 .BI "\-ls3" " gibbs3.pdb "
20 .BI "\-mdata" " mapdata.xvg "
21 .BI "\-g" " shamlog.log "
23 .BI "\-[no]version" ""
35 .BI "\-tsham" " real "
37 .BI "\-dim" " vector "
38 .BI "\-ngrid" " vector "
39 .BI "\-xmin" " vector "
40 .BI "\-xmax" " vector "
45 .BI "\-nlevels" " int "
46 .BI "\-mname" " string "
48 \&\fB g_sham\fR makes multi\-dimensional free\-energy, enthalpy and entropy plots.
49 \&\fB g_sham\fR reads one or more \fB .xvg\fR files and analyzes data sets.
50 \&The basic purpose of \fB g_sham\fR is to plot Gibbs free energy landscapes
51 \&(option \fB \-ls\fR)
52 \&by Bolzmann inverting multi\-dimensional histograms (option \fB \-lp\fR),
54 \&make enthalpy (option \fB \-lsh\fR) and entropy (option \fB \-lss\fR)
55 \&plots. The histograms can be made for any quantities the user supplies.
56 \&A line in the input file may start with a time
57 \&(see option \fB \-time\fR) and any number of \fI y\fR\-values may follow.
58 \&Multiple sets can also be
59 \&read when they are separated by & (option \fB \-n\fR),
60 \&in this case only one \fI y\fR\-value is read from each line.
61 \&All lines starting with and @ are skipped.
65 \&Option \fB \-ge\fR can be used to supply a file with free energies
66 \&when the ensemble is not a Boltzmann ensemble, but needs to be biased
67 \&by this free energy. One free energy value is required for each
68 \&(multi\-dimensional) data point in the \fB \-f\fR input.
72 \&Option \fB \-ene\fR can be used to supply a file with energies.
73 \&These energies are used as a weighting function in the single
74 \&histogram analysis method by Kumar et al. When temperatures
75 \&are supplied (as a second column in the file), an experimental
76 \&weighting scheme is applied. In addition the vales
77 \&are used for making enthalpy and entropy plots.
81 \&With option \fB \-dim\fR, dimensions can be gives for distances.
82 \&When a distance is 2\- or 3\-dimensional, the circumference or surface
83 \&sampled by two particles increases with increasing distance.
84 \&Depending on what one would like to show, one can choose to correct
85 \&the histogram and free\-energy for this volume effect.
86 \&The probability is normalized by r and r2 for dimensions of 2 and 3,
88 \&A value of \-1 is used to indicate an angle in degrees between two
89 \&vectors: a sin(angle) normalization will be applied.
90 \&\fB Note\fR that for angles between vectors the inner\-product or cosine
91 \&is the natural quantity to use, as it will produce bins of the same
94 .BI "\-f" " graph.xvg"
98 .BI "\-ge" " gibbs.xvg"
102 .BI "\-ene" " esham.xvg"
106 .BI "\-dist" " ener.xvg"
110 .BI "\-histo" " edist.xvg"
114 .BI "\-bin" " bindex.ndx"
118 .BI "\-lp" " prob.xpm"
120 X PixMap compatible matrix file
122 .BI "\-ls" " gibbs.xpm"
124 X PixMap compatible matrix file
126 .BI "\-lsh" " enthalpy.xpm"
128 X PixMap compatible matrix file
130 .BI "\-lss" " entropy.xpm"
132 X PixMap compatible matrix file
134 .BI "\-map" " map.xpm"
136 X PixMap compatible matrix file
138 .BI "\-ls3" " gibbs3.pdb"
140 Protein data bank file
142 .BI "\-mdata" " mapdata.xvg"
146 .BI "\-g" " shamlog.log"
152 Print help info and quit
154 .BI "\-[no]version" "no "
155 Print version info and quit
157 .BI "\-nice" " int" " 19"
161 View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files
163 .BI "\-xvg" " enum" " xmgrace"
164 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR
166 .BI "\-[no]time" "yes "
167 Expect a time in the input
169 .BI "\-b" " real" " \-1 "
170 First time to read from set
172 .BI "\-e" " real" " \-1 "
173 Last time to read from set
175 .BI "\-ttol" " real" " 0 "
176 Tolerance on time in appropriate units (usually ps)
178 .BI "\-n" " int" " 1"
179 Read this number of sets separated by lines containing only an ampersand
184 .BI "\-bw" " real" " 0.1 "
185 Binwidth for the distribution
187 .BI "\-[no]sham" "yes "
188 Turn off energy weighting even if energies are given
190 .BI "\-tsham" " real" " 298.15"
191 Temperature for single histogram analysis
193 .BI "\-pmin" " real" " 0 "
194 Minimum probability. Anything lower than this will be set to zero
196 .BI "\-dim" " vector" " 1 1 1"
197 Dimensions for distances, used for volume correction (max 3 values, dimensions 3 will get the same value as the last)
199 .BI "\-ngrid" " vector" " 32 32 32"
200 Number of bins for energy landscapes (max 3 values, dimensions 3 will get the same value as the last)
202 .BI "\-xmin" " vector" " 0 0 0"
203 Minimum for the axes in energy landscape (see above for 3 dimensions)
205 .BI "\-xmax" " vector" " 1 1 1"
206 Maximum for the axes in energy landscape (see above for 3 dimensions)
208 .BI "\-pmax" " real" " 0 "
209 Maximum probability in output, default is calculate
211 .BI "\-gmax" " real" " 0 "
212 Maximum free energy in output, default is calculate
214 .BI "\-emin" " real" " 0 "
215 Minimum enthalpy in output, default is calculate
217 .BI "\-emax" " real" " 0 "
218 Maximum enthalpy in output, default is calculate
220 .BI "\-nlevels" " int" " 25"
221 Number of levels for energy landscape
223 .BI "\-mname" " string" " "
224 Legend label for the custom landscape
229 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.