g_rdf(1)
NAME
g_rdf - calculates radial distribution functions
SYNOPSIS
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 -[no]pbc -[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 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
option -xy
If a run input file is supplied ( -s ), 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.
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
FILES
- -f traj.xtc Input
- Generic trajectory: xtc trr trj gro g96 pdb
- -s topol.tpr Input, Opt.
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
- -n index.ndx Input, Opt.
- Index 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]h no
- 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)
- -[no]w no
- View output xvg, xpm, eps and pdb files
- -[no]xvgr yes
- Add specific codes (legends etc.) in the output xvg files for the
- xmgrace program
- -bin real 0.002
- Binwidth (nm)
- -[no]com no
- RDF with respect to the center of mass of first group
- -[no]pbc yes
- Use periodic boundary conditions for computing distances
- -[no]xy no
- 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
- More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.