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       g_polystat - calculates static properties of polymers

       VERSION 4.0.1


       g_polystat  -s  topol.tpr  -f  traj.xtc -n index.ndx -o polystat.xvg -v
       polyvec.xvg -p persist.xvg -[no]h -nice int -b time -e  time  -dt  time
       -tu enum -[no]w -[no]xvgr -[no]mw -[no]pc


       g_polystat  plots  static  properties of polymers as a function of time
       and prints the average.

       By default it determines the average end-to-end distance and  radii  of
       gyration  of  polymers.  It asks for an index group and split this into
       molecules. The end-to-end distance is then determined using  the  first
       and  the  last  atom  in  the  index group for each molecules.  For the
       radius of gyration the total and the three principal components for the
       average  gyration tensor are written.  With option  -v the eigenvectors
       are written.  With option  -pc also  the  average  eigenvalues  of  the
       individual gyration tensors are written.

       With option  -p the presistence length is determined.  The chosen index
       group should consist of atoms that  are  consecutively  bonded  in  the
       polymer mainchains.  The presistence length is then determined from the
       cosine of the angles between bonds with an  index  difference  that  is
       even,  the  odd  pairs are not used, because straight polymer backbones
       are usually all trans and therefore only every second bond aligns.  The
       persistence  length is defined as number of bonds where the average cos
       reaches  a  value  of  1/e.  This  point  is  determined  by  a  linear
       interpolation of log(cos).


       -s topol.tpr Input
        Run input file: tpr tpb tpa

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

       -n index.ndx Input, Opt.
        Index file

       -o polystat.xvg Output
        xvgr/xmgr file

       -v polyvec.xvg Output, Opt.
        xvgr/xmgr file

       -p persist.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)

       -tu enum ps
        Time unit:  ps,  fs,  ns,  us,  ms or  s

        View output xvg, xpm, eps and pdb files

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

        Use the mass weighting for radii of gyration

        Plot average eigenvalues



       More     information     about     GROMACS     is     available      at

                                Thu 16 Oct 2008                  g_polystat(1)