g_rdf_d (1) - Linux Manuals
g_rdf_d: calculates radial distribution functions
NAMEg_rdf - calculates radial distribution functions
SYNOPSISg_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 real
DESCRIPTIONThe 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.
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.
FILES-f traj.xtc Input
-nice int 19
-b time 0
-e time 0
-dt time 0
-bin real 0.002
-rdf enum atom
-cut real 0
-ng int 1
-fade real 0
-nlevel int 20
-startq real 0
-endq real 60
-energy real 12