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 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

       Options to specify input files:

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

       -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: none, xmgrace, xmgr

       -[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

       2020, GROMACS development team