1GMX-RDF(1) GROMACS GMX-RDF(1)
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6 gmx-rdf - Calculate radial distribution functions
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9 gmx rdf [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
10 [-o [<.xvg>]] [-cn [<.xvg>]] [-b <time>] [-e <time>]
11 [-dt <time>] [-tu <enum>] [-fgroup <selection>] [-xvg <enum>]
12 [-[no]rmpbc] [-[no]pbc] [-sf <file>] [-selrpos <enum>]
13 [-seltype <enum>] [-bin <real>] [-norm <enum>] [-[no]xy]
14 [-[no]excl] [-cut <real>] [-rmax <real>] [-surf <enum>]
15 [-ref <selection>] [-sel <selection>]
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18 gmx rdf calculates radial distribution functions from one reference set
19 of position (set with -ref) to one or more sets of positions (set with
20 -sel). To compute the RDF with respect to the closest position in a
21 set in -ref instead, use -surf: if set, then -ref is partitioned into
22 sets based on the value of -surf, and the closest position in each set
23 is used. To compute the RDF around axes parallel to the z-axis, i.e.,
24 only in the x-y plane, use -xy.
25 To set the bin width and maximum distance to use in the RDF, use -bin
27 and -rmax, respectively. The latter can be used to limit the computa‐
28 tional cost if the RDF is not of interest up to the default (half of
29 the box size with PBC, three times the box size without PBC).
30 To use exclusions from the topology (-s), set -excl and ensure that
32 both -ref and -sel only select atoms. A rougher alternative to exclude
33 intra-molecular peaks is to set -cut to a non-zero value to clear the
34 RDF at small distances.
35 The RDFs are normalized by 1) average number of positions in -ref (the
37 number of groups with -surf), 2) volume of the bin, and 3) average par‐
38 ticle density of -sel positions for that selection. To change the nor‐
39 malization, use -norm:
40 · rdf: Use all factors for normalization. This produces a normal RDF.
42 · number_density: Use the first two factors. This produces a number
44 density as a function of distance.
45 · none: Use only the first factor. In this case, the RDF is only
47 scaled with the bin width to make the integral of the curve represent
48 the number of pairs within a range.
49 Note that exclusions do not affect the normalization: even if -excl is
51 set, or -ref and -sel contain the same selection, the normalization
52 factor is still N*M, not N*(M-excluded).
53 For -surf, the selection provided to -ref must select atoms, i.e., cen‐
55 ters of mass are not supported. Further, -nonorm is implied, as the
56 bins have irregular shapes and the volume of a bin is not easily com‐
57 putable.
58 Option -cn produces the cumulative number RDF, i.e. the average number
60 of particles within a distance r.
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63 Options to specify input files:
64 -f [<.xtc/.trr/…>] (traj.xtc) (Optional)
66 Input trajectory or single configuration: xtc trr cpt gro g96
67 pdb tng
68 -s [<.tpr/.gro/…>] (topol.tpr) (Optional)
70 Input structure: tpr gro g96 pdb brk ent
71 -n [<.ndx>] (index.ndx) (Optional)
73 Extra index groups
74 Options to specify output files:
76 -o [<.xvg>] (rdf.xvg)
78 Computed RDFs
79 -cn [<.xvg>] (rdf_cn.xvg) (Optional)
81 Cumulative RDFs
82 Other options:
84 -b <time> (0)
86 First frame (ps) to read from trajectory
87 -e <time> (0)
89 Last frame (ps) to read from trajectory
90 -dt <time> (0)
92 Only use frame if t MOD dt == first time (ps)
93 -tu <enum> (ps)
95 Unit for time values: fs, ps, ns, us, ms, s
96 -fgroup <selection>
98 Atoms stored in the trajectory file (if not set, assume first N
99 atoms)
100 -xvg <enum> (xmgrace)
102 Plot formatting: none, xmgrace, xmgr
103 -[no]rmpbc (yes)
105 Make molecules whole for each frame
106 -[no]pbc (yes)
108 Use periodic boundary conditions for distance calculation
109 -sf <file>
111 Provide selections from files
112 -selrpos <enum> (atom)
114 Selection reference positions: atom, res_com, res_cog, mol_com,
115 mol_cog, whole_res_com, whole_res_cog, whole_mol_com,
116 whole_mol_cog, part_res_com, part_res_cog, part_mol_com,
117 part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog
118 -seltype <enum> (atom)
120 Default selection output positions: atom, res_com, res_cog,
121 mol_com, mol_cog, whole_res_com, whole_res_cog, whole_mol_com,
122 whole_mol_cog, part_res_com, part_res_cog, part_mol_com,
123 part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog
124 -bin <real> (0.002)
126 Bin width (nm)
127 -norm <enum> (rdf)
129 Normalization: rdf, number_density, none
130 -[no]xy (no)
132 Use only the x and y components of the distance
133 -[no]excl (no)
135 Use exclusions from topology
136 -cut <real> (0)
138 Shortest distance (nm) to be considered
139 -rmax <real> (0)
141 Largest distance (nm) to calculate
142 -surf <enum> (no)
144 RDF with respect to the surface of the reference: no, mol, res
145 -ref <selection>
147 Reference selection for RDF computation
148 -sel <selection>
150 Selections to compute RDFs for from the reference
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153 gmx(1)
154 More information about GROMACS is available at <‐
156 http://www.gromacs.org/>.
157
159 2019, GROMACS development team
1602019.2 Apr 16, 2019 GMX-RDF(1)