g_rdf(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c					  g_rdf(1)

NAME

       g_rdf - calculates radial distribution functions

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       g_rdf -f traj.xtc -s topol.tpr -n index.ndx -d sfactor.dat -o rdf.xvg -sq sq.xvg -cn rdf_cn.xvg -hq hq.xvg -[no]h -[no]version -nice int -b
       time -e time -dt time -[no]w -xvg enum -bin real -[no]com -surf enum -rdf enum -[no]pbc -[no]norm -[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  methods
       are  around  the  center of mass of a set of particles ( -com) or to the closest particle in a set ( -surf).  With all methods, the RDF can
       also be calculated around axes parallel to the  z-axis with option  -xy.  With option  -surf normalization can not be used.

       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  geome-
       try  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.  Weighting other than COM or COG can currently only be achieved by providing a  run  input  file
       with different masses.  Options	-com and  -surf also work 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 e.g. benzene a topology, setting nrexcl to 5 would eliminate all intramolecular con-
       tributions 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.

       To bridge the gap between theory and experiment structure factors can be computed (option  -sq). The algorithm uses FFT, the  grid  spacing
       of which is determined by option  -grid.

FILES

       -f traj.xtc Input
	Trajectory: xtc trr trj gro g96 pdb cpt

       -s topol.tpr Input, Opt.
	Structure+mass(db): tpr tpb tpa gro g96 pdb

       -n index.ndx Input, Opt.
	Index file

       -d sfactor.dat Input, Opt.
	Generic data 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]hno
	Print help info and quit

       -[no]versionno
	Print version 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]wno
	View output  .xvg,  .xpm,  .eps and  .pdb files

       -xvg enum xmgrace
	xvg plot formatting:  xmgrace,	xmgr or  none

       -bin real 0.002
	Binwidth (nm)

       -[no]comno
	RDF with respect to the center of mass of first group

       -surf enum no
	RDF with respect to the surface of the first group:  no,  mol or  res

       -rdf enum atom
	RDF type:  atom,  mol_com,  mol_cog,  res_com or  res_cog

       -[no]pbcyes
	Use periodic boundary conditions for computing distances. Without PBC the maximum range will be three times the largest box edge.

       -[no]normyes
	Normalize for volume and density

       -[no]xyno
	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 GROMACS is available at <http://www.gromacs.org/>.

								  Mon 4 Apr 2011							  g_rdf(1)