g_rdf(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_rdf(1)
NAME
g_rdf - calculates radial distribution functions
VERSION 4.5.4-dev-20110404-bc5695c
SYNOPSIS
g_rdf -f traj.xtc -s topol.tpr -n index.ndx -d sfactor.dat -o rdf.xvg -sq sq.xvg -cn rdf_cn.xvg -hq hq.xvg -[no]h -[no]version -nice int -b
time -e time -dt time -[no]w -xvg enum -bin real -[no]com -surf enum -rdf enum -[no]pbc -[no]norm -[no]xy -cut real -ng int -fade real
-nlevel int -startq real -endq real -energy real
DESCRIPTION
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 methods
are around the center of mass of a set of particles ( -com) or to the closest particle in a set ( -surf). With all methods, the RDF can
also be calculated around axes parallel to the z-axis with option -xy. With option -surf normalization can not be used.
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 geome-
try 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. Weighting other than COM or COG can currently only be achieved by providing a run input file
with different masses. Options -com and -surf also work 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 e.g. benzene a topology, setting nrexcl to 5 would eliminate all intramolecular con-
tributions 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 grid spacing
of which is determined by option -grid.
FILES
-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.
Index file
-d sfactor.dat Input, Opt.
Generic data file
-o rdf.xvg Output, Opt.
xvgr/xmgr file
-sq sq.xvg Output, Opt.
xvgr/xmgr file
-cn rdf_cn.xvg Output, Opt.
xvgr/xmgr file
-hq hq.xvg Output, Opt.
xvgr/xmgr file
OTHER OPTIONS
-[no]hno
Print help info and quit
-[no]versionno
Print version 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)
-[no]wno
View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace
xvg plot formatting: xmgrace, xmgr or none
-bin real 0.002
Binwidth (nm)
-[no]comno
RDF with respect to the center of mass of first group
-surf enum no
RDF with respect to the surface of the first group: no, mol or res
-rdf enum atom
RDF type: atom, mol_com, mol_cog, res_com or res_cog
-[no]pbcyes
Use periodic boundary conditions for computing distances. Without PBC the maximum range will be three times the largest box edge.
-[no]normyes
Normalize for volume and density
-[no]xyno
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)
SEE ALSO
gromacs(7)
More information about GROMACS is available at <http://www.gromacs.org/>.
Mon 4 Apr 2011 g_rdf(1)