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       g_rdf - calculates radial distribution functions

       VERSION 4.0.1


       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 -rdf enum -[no]pbc -[no]norm -[no]xy -cut
       real -ng int -fade real -nlevel int -startq  real  -endq  real  -energy


       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.

       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.  Other weighting than COM  or  COG
       can  currently  only  be  achieved  by  providing a run input file with
       different masses.  Option  -com also works 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  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, 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 gridspacing 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

       -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

       -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

        Add specific codes (legends etc.) in the  output  xvg  files  for  the
       xmgrace program

       -bin real 0.002
        Binwidth (nm)

        RDF with respect to the center of mass of first group

       -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 larges 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

                                Thu 16 Oct 2008                       g_rdf(1)