g_sham(1)

1g_sham(1)                 GROMACS suite, VERSION 4.5                 g_sham(1)
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NAME

6       g_sham - read/write xmgr and xvgr data sets
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8       VERSION 4.5
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SYNOPSIS

11       g_sham  -f graph.xvg -ge gibbs.xvg -ene esham.xvg -dist ener.xvg -histo
12       edist.xvg -bin bindex.ndx -lp prob.xpm -ls gibbs.xpm -lsh  enthalpy.xpm
13       -lss  entropy.xpm  -map  map.xpm  -ls3 gibbs3.pdb -mdata mapdata.xvg -g
14       shamlog.log -[no]h -[no]version -nice int -[no]w -xvg enum -[no]time -b
15       real  -e  real  -ttol real -n int -[no]d -bw real -[no]sham -tsham real
16       -pmin real -dim vector -ngrid vector -xmin vector  -xmax  vector  -pmax
17       real -gmax real -emin real -emax real -nlevels int -mname string
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DESCRIPTION

20       g_sham makes multi-dimensional free-energy, enthalpy and entropy plots.
21       g_sham reads one or more xvg files  and  analyzes  data  sets.   g_sham
22       basic purpose is plotting Gibbs free energy landscapes (option  -ls) by
23       Bolzmann inverting multi-dimensional histograms (option   -lp)  but  it
24       can also make enthalpy (option  -lsh) and entropy (option  -lss) plots.
25       The histograms can be made for any quantities  the  user  supplies.   A
26       line  in  the  input file may start with a time (see option  -time) and
27       any number of y values may follow.  Multiple sets can also be read when
28       they  are separated by & (option  -n), in this case only one y value is
29       read from each line.  All lines starting with  and @ are skipped.
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32       Option  -ge can be used to supply a file with free  energies  when  the
33       ensemble  is  not  a Boltzmann ensemble, but needs to be biased by this
34       free energy. One free energy value is required for  each  (multi-dimen‐
35       sional) data point in the  -f input.
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38       Option   -ene  can be used to supply a file with energies.  These ener‐
39       gies are used as a weighting function in the single histogram  analysis
40       method  due  to Kumar et. al. When also temperatures are supplied (as a
41       second column in the file) an experimental weighting scheme is applied.
42       In addition the vales are used for making enthalpy and entropy plots.
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45       With  option   -dim dimensions can be gives for distances.  When a dis‐
46       tance is 2- or 3-dimensional, the circumference or surface  sampled  by
47       two  particles  increases  with increasing distance.  Depending on what
48       one would like to show, one can choose to  correct  the  histogram  and
49       free-energy for this volume effect.  The probability is normalized by r
50       and r2 for a dimension of 2 and 3 respectively.  A value of -1 is  used
51       to  indicate an angle in degrees between two vectors: a sin(angle) nor‐
52       malization will be applied.  Note that for angles between  vectors  the
53       inner-product or cosine is the natural quantity to use, as it will pro‐
54       duce bins of the same volume.
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FILES

57       -f graph.xvg Input
58        xvgr/xmgr file
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60       -ge gibbs.xvg Input, Opt.
61        xvgr/xmgr file
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63       -ene esham.xvg Input, Opt.
64        xvgr/xmgr file
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66       -dist ener.xvg Output, Opt.
67        xvgr/xmgr file
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69       -histo edist.xvg Output, Opt.
70        xvgr/xmgr file
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72       -bin bindex.ndx Output, Opt.
73        Index file
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75       -lp prob.xpm Output, Opt.
76        X PixMap compatible matrix file
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78       -ls gibbs.xpm Output, Opt.
79        X PixMap compatible matrix file
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81       -lsh enthalpy.xpm Output, Opt.
82        X PixMap compatible matrix file
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84       -lss entropy.xpm Output, Opt.
85        X PixMap compatible matrix file
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87       -map map.xpm Output, Opt.
88        X PixMap compatible matrix file
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90       -ls3 gibbs3.pdb Output, Opt.
91        Protein data bank file
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93       -mdata mapdata.xvg Output, Opt.
94        xvgr/xmgr file
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96       -g shamlog.log Output, Opt.
97        Log file
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OTHER OPTIONS

101       -[no]hno
102        Print help info and quit
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104       -[no]versionno
105        Print version info and quit
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107       -nice int 19
108        Set the nicelevel
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110       -[no]wno
111        View output xvg, xpm, eps and pdb files
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113       -xvg enum xmgrace
114        xvg plot formatting:  xmgrace,  xmgr or  none
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116       -[no]timeyes
117        Expect a time in the input
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119       -b real -1
120        First time to read from set
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122       -e real -1
123        Last time to read from set
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125       -ttol real 0
126        Tolerance on time in appropriate units (usually ps)
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128       -n int 1
129        Read  sets separated by &
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131       -[no]dno
132        Use the derivative
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134       -bw real 0.1
135        Binwidth for the distribution
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137       -[no]shamyes
138        Turn off energy weighting even if energies are given
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140       -tsham real 298.15
141        Temperature for single histogram analysis
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143       -pmin real 0
144        Minimum probability. Anything lower than this will be set to zero
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146       -dim vector 1 1 1
147        Dimensions for distances, used for volume correction  (max  3  values,
148       dimensions  3 will get the same value as the last)
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150       -ngrid vector 32 32 32
151        Number of bins for energy landscapes (max 3 values, dimensions  3 will
152       get the same value as the last)
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154       -xmin vector 0 0 0
155        Minimum for the axes in energy landscape (see above for  3 dimensions)
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157       -xmax vector 1 1 1
158        Maximum for the axes in energy landscape (see above for  3 dimensions)
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160       -pmax real 0
161        Maximum probability in output, default is calculate
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163       -gmax real 0
164        Maximum free energy in output, default is calculate
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166       -emin real 0
167        Minimum enthalpy in output, default is calculate
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169       -emax real 0
170        Maximum enthalpy in output, default is calculate
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172       -nlevels int 25
173        Number of levels for energy landscape
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175       -mname string
176        Legend label for the custom landscape
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NAME

SYNOPSIS

DESCRIPTION

FILES

OTHER OPTIONS

SEE ALSO