NAME

       g_polystat - calculates static properties of polymers

       VERSION 4.6.5

SYNOPSIS

       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

DESCRIPTION

        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  -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).

FILES

       -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

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)

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

       -[no]wno
        View output  .xvg,  .xpm,  .eps and  .pdb files

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

       -[no]mwyes
        Use the mass weighting for radii of gyration

       -[no]pcno
        Plot average eigenvalues

SEE ALSO

       gromacs(7)

       More information about GROMACS is available at <http://www.gromacs.org/>.

                                                 Mon 2 Dec 2013                                    g_polystat(1)