g_rdf(1)

NAME
g_rdf VERSION 3.2.0

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 -bin real -[no]com -cut real -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. 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 -1
 First frame (ps) to read from trajectory -e time -1
 Last frame (ps) to read from trajectory -dt time -1
 Only use frame when t MOD dt = first time (ps) -[no]w no
 View output xvg, xpm, eps and pdb files -bin real 0.001
 Binwidth (nm) -[no]com no
 RDF with respect to the center of mass of first group -cut real 0
 Shortest distance (nm) to be considered -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)