1 .TH g_rdf 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
3 g_rdf - calculates radial distribution functions
5 .B VERSION 4.5.4-dev-20110404-bc5695c
9 .BI "\-s" " topol.tpr "
10 .BI "\-n" " index.ndx "
11 .BI "\-d" " sfactor.dat "
14 .BI "\-cn" " rdf_cn.xvg "
17 .BI "\-[no]version" ""
34 .BI "\-nlevel" " int "
35 .BI "\-startq" " real "
37 .BI "\-energy" " real "
39 \&The structure of liquids can be studied by either neutron or X\-ray
40 \&scattering. The most common way to describe liquid structure is by a
41 \&radial distribution function. However, this is not easy to obtain from
42 \&a scattering experiment.
45 \&\fB g_rdf\fR calculates radial distribution functions in different ways.
46 \&The normal method is around a (set of) particle(s), the other methods
47 \&are around the center of mass of a set of particles (\fB \-com\fR)
48 \&or to the closest particle in a set (\fB \-surf\fR).
49 \&With all methods, the RDF can also be calculated around axes parallel
50 \&to the \fI z\fR\-axis with option \fB \-xy\fR.
51 \&With option \fB \-surf\fR normalization can not be used.
54 \&The option \fB \-rdf\fR sets the type of RDF to be computed.
55 \&Default is for atoms or particles, but one can also select center
56 \&of mass or geometry of molecules or residues. In all cases, only
57 \&the atoms in the index groups are taken into account.
58 \&For molecules and/or the center of mass option, a run input file
60 \&Weighting other than COM or COG can currently only be achieved
61 \&by providing a run input file with different masses.
62 \&Options \fB \-com\fR and \fB \-surf\fR also work in conjunction
66 \&If a run input file is supplied (\fB \-s\fR) and \fB \-rdf\fR is set
67 \&to \fB atom\fR, exclusions defined
68 \&in that file are taken into account when calculating the RDF.
69 \&The option \fB \-cut\fR is meant as an alternative way to avoid
70 \&intramolecular peaks in the RDF plot.
71 \&It is however better to supply a run input file with a higher number of
72 \&exclusions. For e.g. benzene a topology, setting nrexcl to 5
73 \&would eliminate all intramolecular contributions to the RDF.
74 \&Note that all atoms in the selected groups are used, also the ones
75 \&that don't have Lennard\-Jones interactions.
78 \&Option \fB \-cn\fR produces the cumulative number RDF,
79 \&i.e. the average number of particles within a distance r.
82 \&To bridge the gap between theory and experiment structure factors can
83 \&be computed (option \fB \-sq\fR). The algorithm uses FFT, the grid
84 \&spacing of which is determined by option \fB \-grid\fR.
88 Trajectory: xtc trr trj gro g96 pdb cpt
90 .BI "\-s" " topol.tpr"
92 Structure+mass(db): tpr tpb tpa gro g96 pdb
94 .BI "\-n" " index.ndx"
98 .BI "\-d" " sfactor.dat"
110 .BI "\-cn" " rdf_cn.xvg"
120 Print help info and quit
122 .BI "\-[no]version" "no "
123 Print version info and quit
125 .BI "\-nice" " int" " 19"
128 .BI "\-b" " time" " 0 "
129 First frame (ps) to read from trajectory
131 .BI "\-e" " time" " 0 "
132 Last frame (ps) to read from trajectory
134 .BI "\-dt" " time" " 0 "
135 Only use frame when t MOD dt = first time (ps)
138 View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files
140 .BI "\-xvg" " enum" " xmgrace"
141 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR
143 .BI "\-bin" " real" " 0.002 "
146 .BI "\-[no]com" "no "
147 RDF with respect to the center of mass of first group
149 .BI "\-surf" " enum" " no"
150 RDF with respect to the surface of the first group: \fB no\fR, \fB mol\fR or \fB res\fR
152 .BI "\-rdf" " enum" " atom"
153 RDF type: \fB atom\fR, \fB mol_com\fR, \fB mol_cog\fR, \fB res_com\fR or \fB res_cog\fR
155 .BI "\-[no]pbc" "yes "
156 Use periodic boundary conditions for computing distances. Without PBC the maximum range will be three times the largest box edge.
158 .BI "\-[no]norm" "yes "
159 Normalize for volume and density
162 Use only the x and y components of the distance
164 .BI "\-cut" " real" " 0 "
165 Shortest distance (nm) to be considered
167 .BI "\-ng" " int" " 1"
168 Number of secondary groups to compute RDFs around a central group
170 .BI "\-fade" " real" " 0 "
171 From this distance onwards the RDF is tranformed by g'(r) = 1 + [g(r)\-1] exp(\-(r/fade\-1)2 to make it go to 1 smoothly. If fade is 0.0 nothing is done.
173 .BI "\-nlevel" " int" " 20"
174 Number of different colors in the diffraction image
176 .BI "\-startq" " real" " 0 "
179 .BI "\-endq" " real" " 60 "
182 .BI "\-energy" " real" " 12 "
183 Energy of the incoming X\-ray (keV)
188 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.