1GMX-SHAM(1)                         GROMACS                        GMX-SHAM(1)
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NAME

6       gmx-sham - Compute free energies or other histograms from histograms
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SYNOPSIS

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>]
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DESCRIPTION

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.
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33       Option -ge can be used to supply a file with free energies when the en‐
34       semble is not a Boltzmann ensemble, but needs to be biased by this free
35       energy.  One free energy value is required for each (multi-dimensional)
36       data point in the -f input.
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38       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.
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44       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.
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OPTIONS

56       Options to specify input files:
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58       -f [<.xvg>] (graph.xvg)
59              xvgr/xmgr file
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61       -ge [<.xvg>] (gibbs.xvg) (Optional)
62              xvgr/xmgr file
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64       -ene [<.xvg>] (esham.xvg) (Optional)
65              xvgr/xmgr file
66
67       Options to specify output files:
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69       -dist [<.xvg>] (ener.xvg) (Optional)
70              xvgr/xmgr file
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72       -histo [<.xvg>] (edist.xvg) (Optional)
73              xvgr/xmgr file
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75       -bin [<.ndx>] (bindex.ndx) (Optional)
76              Index file
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78       -lp [<.xpm>] (prob.xpm) (Optional)
79              X PixMap compatible matrix file
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81       -ls [<.xpm>] (gibbs.xpm) (Optional)
82              X PixMap compatible matrix file
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84       -lsh [<.xpm>] (enthalpy.xpm) (Optional)
85              X PixMap compatible matrix file
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87       -lss [<.xpm>] (entropy.xpm) (Optional)
88              X PixMap compatible matrix file
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90       -ls3 [<.pdb>] (gibbs3.pdb) (Optional)
91              Protein data bank file
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93       -g [<.log>] (shamlog.log) (Optional)
94              Log file
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96       Other options:
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98       -[no]w (no)
99              View output .xvg, .xpm, .eps and .pdb files
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101       -xvg <enum> (xmgrace)
102              xvg plot formatting: xmgrace, xmgr, none
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104       -[no]time (yes)
105              Expect a time in the input
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107       -b <real> (-1)
108              First time to read from set
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110       -e <real> (-1)
111              Last time to read from set
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113       -ttol <real> (0)
114              Tolerance on time in appropriate units (usually ps)
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116       -n <int> (1)
117              Read  this  number of sets separated by lines containing only an
118              ampersand
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120       -[no]d (no)
121              Use the derivative
122
123       -[no]sham (yes)
124              Turn off energy weighting even if energies are given
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126       -tsham <real> (298.15)
127              Temperature for single histogram analysis
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129       -pmin <real> (0)
130              Minimum probability. Anything lower than this  will  be  set  to
131              zero
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133       -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)
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137       -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)
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141       -xmin <vector> (0 0 0)
142              Minimum  for the axes in energy landscape (see above for > 3 di‐
143              mensions)
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145       -xmax <vector> (1 1 1)
146              Maximum for the axes in energy landscape (see above for > 3  di‐
147              mensions)
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149       -pmax <real> (0)
150              Maximum probability in output, default is calculate
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152       -gmax <real> (0)
153              Maximum free energy in output, default is calculate
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155       -emin <real> (0)
156              Minimum enthalpy in output, default is calculate
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158       -emax <real> (0)
159              Maximum enthalpy in output, default is calculate
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161       -nlevels <int> (25)
162              Number of levels for energy landscape
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SEE ALSO

165       gmx(1)
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167       More     information    about    GROMACS    is    available    at    <‐
168       http://www.gromacs.org/>.
169
171       2022, GROMACS development team
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1762022.3                           Sep 02, 2022                      GMX-SHAM(1)
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