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


       g_polystat - calculates static properties of polymers

       VERSION 4.6.5


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


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

       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  -i the mean square internal distances are written.

       With option  -p the persistence length is  determined.   The  chosen  index  group  should
       consist of atoms that are consecutively bonded in the polymer mainchains.  The persistence
       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

       -i intdist.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)

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

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

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

        Use the mass weighting for radii of gyration

        Plot average eigenvalues



       More information about GROMACS is available at <>.

                                          Mon 2 Dec 2013                            g_polystat(1)