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GMX-RDF(1) |
GROMACS |
GMX-RDF(1) |
gmx-rdf - Calculate radial distribution functions
gmx rdf [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
[-o [<.xvg>]] [-cn [<.xvg>]] [-b <time>] [-e <time>]
[-dt <time>] [-tu <enum>] [-fgroup <selection>] [-xvg <enum>]
[-[no]rmpbc] [-[no]pbc] [-sf <file>] [-selrpos <enum>]
[-seltype <enum>] [-bin <real>] [-norm <enum>] [-[no]xy]
[-[no]excl] [-cut <real>] [-rmax <real>] [-surf <enum>]
[-ref <selection>] [-sel <selection>]
gmx rdf calculates radial distribution functions from one
reference set of position (set with -ref) to one or more sets of
positions (set with -sel). To compute the RDF with respect to the
closest position in a set in -ref instead, use -surf: if set,
then -ref is partitioned into sets based on the value of
-surf, and the closest position in each set is used. To compute the
RDF around axes parallel to the z-axis, i.e., only in the
x-y plane, use -xy.
To set the bin width and maximum distance to use in the RDF, use
-bin and -rmax, respectively. The latter can be used to limit
the computational cost if the RDF is not of interest up to the default (half
of the box size with PBC, three times the box size without PBC).
To use exclusions from the topology (-s), set -excl
and ensure that both -ref and -sel only select atoms. A
rougher alternative to exclude intra-molecular peaks is to set -cut
to a non-zero value to clear the RDF at small distances.
The RDFs are normalized by 1) average number of positions in
-ref (the number of groups with -surf), 2) volume of the bin,
and 3) average particle density of -sel positions for that selection.
To change the normalization, use -norm:
- rdf: Use all factors for normalization. This produces a normal
RDF.
- number_density: Use the first two factors. This produces a number
density as a function of distance.
- none: Use only the first factor. In this case, the RDF is only
scaled with the bin width to make the integral of the curve represent the
number of pairs within a range.
Note that exclusions do not affect the normalization: even if
-excl is set, or -ref and -sel contain the same
selection, the normalization factor is still N*M, not N*(M-excluded).
For -surf, the selection provided to -ref must
select atoms, i.e., centers of mass are not supported. Further,
-nonorm is implied, as the bins have irregular shapes and the volume
of a bin is not easily computable.
Option -cn produces the cumulative number RDF, i.e. the
average number of particles within a distance r.
Options to specify input files:
Options to specify output files:
Other options:
- -b <time>
(0)
- First frame (ps) to read from trajectory
- -e <time>
(0)
- Last frame (ps) to read from trajectory
- -dt <time>
(0)
- Only use frame if t MOD dt == first time (ps)
- -tu <enum>
(ps)
- Unit for time values: fs, ps, ns, us, ms, s
- -fgroup
<selection>
- Atoms stored in the trajectory file (if not set, assume first N
atoms)
- -xvg <enum>
(xmgrace)
- Plot formatting: xmgrace, xmgr, none
- -[no]rmpbc (yes)
- Make molecules whole for each frame
- -[no]pbc (yes)
- Use periodic boundary conditions for distance calculation
- -sf
<file>
- Provide selections from files
- -selrpos
<enum> (atom)
- Selection reference positions: atom, res_com, res_cog, mol_com, mol_cog,
whole_res_com, whole_res_cog, whole_mol_com, whole_mol_cog, part_res_com,
part_res_cog, part_mol_com, part_mol_cog, dyn_res_com, dyn_res_cog,
dyn_mol_com, dyn_mol_cog
- -seltype
<enum> (atom)
- Default selection output positions: atom, res_com, res_cog, mol_com,
mol_cog, whole_res_com, whole_res_cog, whole_mol_com, whole_mol_cog,
part_res_com, part_res_cog, part_mol_com, part_mol_cog, dyn_res_com,
dyn_res_cog, dyn_mol_com, dyn_mol_cog
- -bin <real>
(0.002)
- Bin width (nm)
- -norm <enum>
(rdf)
- Normalization: rdf, number_density, none
- -[no]xy (no)
- Use only the x and y components of the distance
- -[no]excl (no)
- Use exclusions from topology
- -cut <real>
(0)
- Shortest distance (nm) to be considered
- -rmax <real>
(0)
- Largest distance (nm) to calculate
- -surf <enum>
(no)
- RDF with respect to the surface of the reference: no, mol, res
- -ref
<selection>
- Reference selection for RDF computation
- -sel
<selection>
- Selections to compute RDFs for from the reference
gmx(1)
More information about GROMACS is available at
<http://www.gromacs.org/>.
2025, GROMACS development team
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