man g_rdf (Commandes) - g_rdf VERSION 3.3_beta_20050823
NAME
g_rdf VERSION 3.3_beta_20050823
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)