NAME

       gmx-polystat - Calculate static properties of polymers

SYNOPSIS

          gmx polystat [-s [<.tpr>]] [-f [<.xtc/.trr/...>]] [-n [<.ndx>]]
                       [-o [<.xvg>]] [-v [<.xvg>]] [-p [<.xvg>]] [-i [<.xvg>]]
                       [-b <time>] [-e <time>] [-dt <time>] [-tu <enum>]
                       [-[no]w] [-xvg <enum>] [-[no]mw] [-[no]pc]

DESCRIPTION

       gmx  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>).

OPTIONS

       Options to specify input files:

       -s [<.tpr>] (topol.tpr)
              Portable xdr run input file

       -f [<.xtc/.trr/...>] (traj.xtc)
              Trajectory: xtc trr cpt gro g96 pdb tng

       -n [<.ndx>] (index.ndx) (Optional)
              Index file

       Options to specify output files:

       -o [<.xvg>] (polystat.xvg)
              xvgr/xmgr file

       -v [<.xvg>] (polyvec.xvg) (Optional)
              xvgr/xmgr file

       -p [<.xvg>] (persist.xvg) (Optional)
              xvgr/xmgr file

       -i [<.xvg>] (intdist.xvg) (Optional)
              xvgr/xmgr file

       Other options:

       -b <time> (0)
              Time of first frame to read from trajectory (default unit ps)

       -e <time> (0)
              Time of last frame to read from trajectory (default unit ps)

       -dt <time> (0)
              Only use frame when t MOD dt = first time (default unit ps)

       -tu <enum> (ps)
              Unit for time values: fs, ps, ns, us, ms, s

       -[no]w (no)
              View output .xvg, .xpm, .eps and .pdb files

       -xvg <enum> (xmgrace)
              xvg plot formatting: xmgrace, xmgr, none

       -[no]mw (yes)
              Use the mass weighting for radii of gyration

       -[no]pc (no)
              Plot average eigenvalues

SEE ALSO

       gmx(1)

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

COPYRIGHT

       2024, GROMACS development team