Provided by: gromacs-data_2019.3-2_all bug

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

       2019, GROMACS development team