1GMX-SHAM(1) GROMACS GMX-SHAM(1)
2
6 gmx-sham - Compute free energies or other histograms from histograms
7
9 gmx sham [-f [<.xvg>]] [-ge [<.xvg>]] [-ene [<.xvg>]] [-dist [<.xvg>]]
10 [-histo [<.xvg>]] [-bin [<.ndx>]] [-lp [<.xpm>]]
11 [-ls [<.xpm>]] [-lsh [<.xpm>]] [-lss [<.xpm>]]
12 [-ls3 [<.pdb>]] [-g [<.log>]] [-[no]w] [-xvg <enum>]
13 [-[no]time] [-b <real>] [-e <real>] [-ttol <real>]
14 [-n <int>] [-[no]d] [-[no]sham] [-tsham <real>]
15 [-pmin <real>] [-dim <vector>] [-ngrid <vector>]
16 [-xmin <vector>] [-xmax <vector>] [-pmax <real>]
17 [-gmax <real>] [-emin <real>] [-emax <real>]
18 [-nlevels <int>]
19
21 gmx sham makes multi-dimensional free-energy, enthalpy and entropy
22 plots. gmx sham reads one or more .xvg files and analyzes data sets.
23 The basic purpose of gmx sham is to plot Gibbs free energy landscapes
24 (option -ls) by Bolzmann inverting multi-dimensional histograms (option
25 -lp), but it can also make enthalpy (option -lsh) and entropy (option
26 -lss) plots. The histograms can be made for any quantities the user
27 supplies. A line in the input file may start with a time (see option
28 -time) and any number of y-values may follow. Multiple sets can also
29 be read when they are separated by & (option -n), in this case only one
30 y-value is read from each line. All lines starting with # and @ are
31 skipped.
32 Option -ge can be used to supply a file with free energies when the
34 ensemble is not a Boltzmann ensemble, but needs to be biased by this
35 free energy. One free energy value is required for each (multi-dimen‐
36 sional) data point in the -f input.
37 Option -ene can be used to supply a file with energies. These energies
39 are used as a weighting function in the single histogram analysis
40 method by Kumar et al. When temperatures are supplied (as a second col‐
41 umn in the file), an experimental weighting scheme is applied. In addi‐
42 tion the vales are used for making enthalpy and entropy plots.
43 With option -dim, dimensions can be gives for distances. When a dis‐
45 tance is 2- or 3-dimensional, the circumference or surface sampled by
46 two particles increases with increasing distance. Depending on what
47 one would like to show, one can choose to correct the histogram and
48 free-energy for this volume effect. The probability is normalized by r
49 and r^2 for dimensions of 2 and 3, respectively. A value of -1 is used
50 to indicate an angle in degrees between two vectors: a sin(angle) nor‐
51 malization will be applied. Note that for angles between vectors the
52 inner-product or cosine is the natural quantity to use, as it will pro‐
53 duce bins of the same volume.
54
56 Options to specify input files:
57 -f [<.xvg>] (graph.xvg)
59 xvgr/xmgr file
60 -ge [<.xvg>] (gibbs.xvg) (Optional)
62 xvgr/xmgr file
63 -ene [<.xvg>] (esham.xvg) (Optional)
65 xvgr/xmgr file
66 Options to specify output files:
68 -dist [<.xvg>] (ener.xvg) (Optional)
70 xvgr/xmgr file
71 -histo [<.xvg>] (edist.xvg) (Optional)
73 xvgr/xmgr file
74 -bin [<.ndx>] (bindex.ndx) (Optional)
76 Index file
77 -lp [<.xpm>] (prob.xpm) (Optional)
79 X PixMap compatible matrix file
80 -ls [<.xpm>] (gibbs.xpm) (Optional)
82 X PixMap compatible matrix file
83 -lsh [<.xpm>] (enthalpy.xpm) (Optional)
85 X PixMap compatible matrix file
86 -lss [<.xpm>] (entropy.xpm) (Optional)
88 X PixMap compatible matrix file
89 -ls3 [<.pdb>] (gibbs3.pdb) (Optional)
91 Protein data bank file
92 -g [<.log>] (shamlog.log) (Optional)
94 Log file
95 Other options:
97 -[no]w (no)
99 View output .xvg, .xpm, .eps and .pdb files
100 -xvg <enum> (xmgrace)
102 xvg plot formatting: xmgrace, xmgr, none
103 -[no]time (yes)
105 Expect a time in the input
106 -b <real> (-1)
108 First time to read from set
109 -e <real> (-1)
111 Last time to read from set
112 -ttol <real> (0)
114 Tolerance on time in appropriate units (usually ps)
115 -n <int> (1)
117 Read this number of sets separated by lines containing only an
118 ampersand
119 -[no]d (no)
121 Use the derivative
122 -[no]sham (yes)
124 Turn off energy weighting even if energies are given
125 -tsham <real> (298.15)
127 Temperature for single histogram analysis
128 -pmin <real> (0)
130 Minimum probability. Anything lower than this will be set to
131 zero
132 -dim <vector> (1 1 1)
134 Dimensions for distances, used for volume correction (max 3 val‐
135 ues, dimensions > 3 will get the same value as the last)
136 -ngrid <vector> (32 32 32)
138 Number of bins for energy landscapes (max 3 values, dimensions >
139 3 will get the same value as the last)
140 -xmin <vector> (0 0 0)
142 Minimum for the axes in energy landscape (see above for > 3
143 dimensions)
144 -xmax <vector> (1 1 1)
146 Maximum for the axes in energy landscape (see above for > 3
147 dimensions)
148 -pmax <real> (0)
150 Maximum probability in output, default is calculate
151 -gmax <real> (0)
153 Maximum free energy in output, default is calculate
154 -emin <real> (0)
156 Minimum enthalpy in output, default is calculate
157 -emax <real> (0)
159 Maximum enthalpy in output, default is calculate
160 -nlevels <int> (25)
162 Number of levels for energy landscape
163
165 gmx(1)
166 More information about GROMACS is available at <‐
168 http://www.gromacs.org/>.
169
171 2019, GROMACS development team
1722018.7 May 29, 2019 GMX-SHAM(1)