g_rdf - calculates radial distribution functions
g_rdf -f traj.xtc -s topol.tpr -n index.ndx -o rdf.xvg -sq sq.xvg -cn
rdf_cn.xvg -hq hq.xvg -[no]h -nice int -b time -e time -dt time -[no]w
-[no]xvgr -bin real -[no]com -rdf enum -[no]pbc -[no]norm -[no]xy -cut
real -ng int -fade real -nlevel int -startq real -endq real -energy
The structure of liquids can be studied by either neutron or X-ray
scattering. The most common way to describe liquid structure is by a
radial distribution function. However, this is not easy to obtain from
a scattering experiment.
g_rdf calculates radial distribution functions in different ways. The
normal method is around a (set of) particle(s), the other method is
around the center of mass of a set of particles. With both methods
rdf’s can also be calculated around axes parallel to the z-axis with
The option -rdf sets the type of rdf to be computed. Default is for
atoms or particles, but one can also select center of mass or geometry
of molecules or residues. In all cases only the atoms in the index
groups are taken into account. For molecules and/or the center of mass
option a run input file is required. Other weighting than COM or COG
can currently only be achieved by providing a run input file with
different masses. Option -com also works in conjunction with -rdf.
If a run input file is supplied ( -s) and -rdf is set to atom,
exclusions defined in that file are taken into account when calculating
the rdf. The option -cut is meant as an alternative way to avoid
intramolecular peaks in the rdf plot. It is however better to supply a
run input file with a higher number of exclusions. For eg. benzene a
topology with nrexcl set to 5 would eliminate all intramolecular
contributions to the rdf. Note that all atoms in the selected groups
are used, also the ones that don’t have Lennard-Jones interactions.
Option -cn produces the cumulative number rdf, i.e. the average number
of particles within a distance r.
To bridge the gap between theory and experiment structure factors can
be computed (option -sq). The algorithm uses FFT, the gridspacing of
which is determined by option -grid.
-f traj.xtc Input
Trajectory: xtc trr trj gro g96 pdb cpt
-s topol.tpr Input, Opt.
Structure+mass(db): tpr tpb tpa gro g96 pdb
-n index.ndx Input, Opt.
-o rdf.xvg Output, Opt.
-sq sq.xvg Output, Opt.
-cn rdf_cn.xvg Output, Opt.
-hq hq.xvg Output, Opt.
Print help info and quit
-nice int 19
Set the nicelevel
-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 when t MOD dt = first time (ps)
View output xvg, xpm, eps and pdb files
Add specific codes (legends etc.) in the output xvg files for the
-bin real 0.002
RDF with respect to the center of mass of first group
-rdf enum atom
RDF type: atom, mol_com, mol_cog, res_com or res_cog
Use periodic boundary conditions for computing distances. Without PBC
the maximum range will be three times the larges box edge.
Normalize for volume and density
Use only the x and y components of the distance
-cut real 0
Shortest distance (nm) to be considered
-ng int 1
Number of secondary groups to compute RDFs around a central group
-fade real 0
From this distance onwards the RDF is tranformed by g’(r) = 1 +
[g(r)-1] exp(-(r/fade-1)2 to make it go to 1 smoothly. If fade is 0.0
nothing is done.
-nlevel int 20
Number of different colors in the diffraction image
-startq real 0
Starting q (1/nm)
-endq real 60
Ending q (1/nm)
-energy real 12
Energy of the incoming X-ray (keV)
More information about GROMACS is available at
Thu 16 Oct 2008 g_rdf(1)