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gmx-polystat - Calculate static properties of polymers


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]


gmx 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>).


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)
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)
Unit for time values: fs, ps, ns, us, ms, s

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

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

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

-[no]pc (no)
Plot average eigenvalues

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