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GMX-RDF(1)			     GROMACS			      GMX-RDF(1)

NAME
     gmx-rdf - Calculate radial distribution functions

SYNOPSIS
	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>]

DESCRIPTION
     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 in-
     tra-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 num-
     ber  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 den-
       sity 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
     Options to specify input files:

     -f [<.xtc/.trr/...>] (traj.xtc) (Optional)
	    Input  trajectory  or  single configuration: xtc trr cpt gro g96 pdb
	    tng h5md

     -s [<.tpr/.gro/...>] (topol.tpr) (Optional)
	    Input structure: tpr gro g96 pdb brk ent

     -n [<.ndx>] (index.ndx) (Optional)
	    Extra index groups

     Options to specify output files:

     -o [<.xvg>] (rdf.xvg)
	    Computed RDFs

     -cn [<.xvg>] (rdf_cn.xvg) (Optional)
	    Cumulative RDFs

     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

SEE ALSO
     gmx(1)

     More information about GROMACS is available at <http://www.gromacs.org/>.

COPYRIGHT
     2026, GROMACS development team

2026.3				  Jun 25, 2026			      GMX-RDF(1)
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