Provided by: gromacs-data_4.6.5-1build1_all bug


       g_rdf - calculates radial distribution functions

       VERSION 4.6.5


       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


       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.


       -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


        Print help info and quit

        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)

        View output  .xvg,  .xpm,  .eps and  .pdb files

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

       -bin real 0.002
        Binwidth (nm)

        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

        Use  periodic  boundary conditions for computing distances. Without PBC the maximum range
       will be three times the largest box edge.

        Normalize for volume and density

        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)



       More information about GROMACS is available at <>.

                                          Mon 2 Dec 2013                                 g_rdf(1)