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g_rdf_d
Langue: en
Version: 261116 (debian - 07/07/09)
Section: 1 (Commandes utilisateur)
NAME
g_rdf - calculates radial distribution functionsSYNOPSIS
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 realDESCRIPTION
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 InputGeneric 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 noPrint 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/>.
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre