NAME

       g_rdf - calculates radial distribution functions

       VERSION 4.6.5

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 geometry 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
       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, 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 2 Dec 2013                                         g_rdf(1)