g_rdf_d

Langue: en

Autres versions - même langue

Version: 261116 (debian - 07/07/09)

Section: 1 (Commandes utilisateur)

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

gromacs(7)

More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.