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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 computa-
       tional 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 par-
       ticle density of	-sel positions for that	selection. To change the  nor-
       malization, 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., cen-
       ters  of	 mass  are  not	supported. Further, -nonorm is implied,	as the
       bins have irregular shapes and the volume of a bin is not  easily  com-
       putable.

       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: 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
       2025, GROMACS development team

2025.0				 Feb 10, 2025			    GMX-RDF(1)

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