g_rdf(1) - f14

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

6       g_rdf - calculates radial distribution functions
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8       VERSION 4.5
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SYNOPSIS

11       g_rdf  -f  traj.xtc -s topol.tpr -n index.ndx -d sfactor.dat -o rdf.xvg
12       -sq sq.xvg -cn rdf_cn.xvg -hq hq.xvg -[no]h -[no]version -nice  int  -b
13       time  -e  time  -dt time -[no]w -xvg enum -bin real -[no]com -surf enum
14       -rdf enum -[no]pbc -[no]norm -[no]xy  -cut  real  -ng  int  -fade  real
15       -nlevel int -startq real -endq real -energy real
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DESCRIPTION

18       The  structure  of  liquids  can  be studied by either neutron or X-ray
19       scattering. The most common way to describe liquid structure  is  by  a
20       radial  distribution function. However, this is not easy to obtain from
21       a scattering experiment.
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24       g_rdf calculates radial distribution functions in different ways.   The
25       normal  method  is around a (set of) particle(s), the other methods are
26       around the center of mass of a set of particles ( -com) or to the clos‐
27       est  particle  in  a  set ( -surf).  With all methods rdf's can also be
28       calculated around axes parallel to the z-axis with option   -xy.   With
29       option  -surf normalization can not be used.
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32       The  option   -rdf sets the type of rdf to be computed.  Default is for
33       atoms or particles, but one can also select center of mass or  geometry
34       of  molecules  or  residues.  In  all cases only the atoms in the index
35       groups are taken into account.  For molecules and/or the center of mass
36       option  a  run input file is required.  Other weighting than COM or COG
37       can currently only be achieved by providing a run input file with  dif‐
38       ferent  masses.  Options  -com and  -surf also work in conjunction with
39       -rdf.
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42       If a run input file is supplied ( -s) and  -rdf is set to  atom, exclu‐
43       sions  defined in that file are taken into account when calculating the
44       rdf.  The option   -cut  is  meant  as  an  alternative  way  to  avoid
45       intramolecular peaks in the rdf plot.  It is however better to supply a
46       run input file with a higher number of exclusions. For  eg.  benzene  a
47       topology  with  nrexcl set to 5 would eliminate all intramolecular con‐
48       tributions to the rdf.  Note that all atoms in the selected groups  are
49       used, also the ones that don't have Lennard-Jones interactions.
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52       Option  -cn produces the cumulative number rdf, i.e. the average number
53       of particles within a distance r.
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56       To bridge the gap between theory and experiment structure  factors  can
57       be  computed (option  -sq). The algorithm uses FFT, the grid spacing of
58       which is determined by option  -grid.
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FILES

61       -f traj.xtc Input
62        Trajectory: xtc trr trj gro g96 pdb cpt
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64       -s topol.tpr Input, Opt.
65        Structure+mass(db): tpr tpb tpa gro g96 pdb
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67       -n index.ndx Input, Opt.
68        Index file
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70       -d sfactor.dat Input, Opt.
71        Generic data file
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73       -o rdf.xvg Output, Opt.
74        xvgr/xmgr file
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76       -sq sq.xvg Output, Opt.
77        xvgr/xmgr file
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79       -cn rdf_cn.xvg Output, Opt.
80        xvgr/xmgr file
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82       -hq hq.xvg Output, Opt.
83        xvgr/xmgr file
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OTHER OPTIONS

87       -[no]hno
88        Print help info and quit
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90       -[no]versionno
91        Print version info and quit
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93       -nice int 19
94        Set the nicelevel
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96       -b time 0
97        First frame (ps) to read from trajectory
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99       -e time 0
100        Last frame (ps) to read from trajectory
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102       -dt time 0
103        Only use frame when t MOD dt = first time (ps)
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105       -[no]wno
106        View output xvg, xpm, eps and pdb files
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108       -xvg enum xmgrace
109        xvg plot formatting:  xmgrace,  xmgr or  none
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111       -bin real 0.002
112        Binwidth (nm)
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114       -[no]comno
115        RDF with respect to the center of mass of first group
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117       -surf enum no
118        RDF with respect to the surface of the first group:  no,  mol or  res
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120       -rdf enum atom
121        RDF type:  atom,  mol_com,  mol_cog,  res_com or  res_cog
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123       -[no]pbcyes
124        Use periodic boundary conditions for computing distances. Without  PBC
125       the maximum range will be three times the largest box edge.
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127       -[no]normyes
128        Normalize for volume and density
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130       -[no]xyno
131        Use only the x and y components of the distance
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133       -cut real 0
134        Shortest distance (nm) to be considered
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136       -ng int 1
137        Number of secondary groups to compute RDFs around a central group
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139       -fade real 0
140        From  this  distance  onwards  the  RDF  is  tranformed by g'(r) = 1 +
141       [g(r)-1] exp(-(r/fade-1)2 to make it go to 1 smoothly. If fade  is  0.0
142       nothing is done.
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144       -nlevel int 20
145        Number of different colors in the diffraction image
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147       -startq real 0
148        Starting q (1/nm)
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150       -endq real 60
151        Ending q (1/nm)
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153       -energy real 12
154        Energy of the incoming X-ray (keV)
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NAME

SYNOPSIS

DESCRIPTION

FILES

OTHER OPTIONS

SEE ALSO