gmx-polystat(1) GROMACS Manual gmx-polystat(1)NAMEgmx-polystat - Calculate static properties of polymers
SYNOPSIS
gmx polystat [-s [<.tpr/.tpb/...>]] [-f [<.xtc/.trr/...>]]
[-n [<.ndx>]] [-o [<.xvg>]] [-v [<.xvg>]] [-p [<.xvg>]]
[-i [<.xvg>]] [-nice <int>] [-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 aver‐
age 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 interpola‐
tion of log(cos).
OPTIONS
Options to specify input and output files:
-s [<.tpr/.tpb/...>] (topol.tpr) (Input)
Run input file: tpr tpb tpa
-f [<.xtc/.trr/...>] (traj.xtc) (Input)
Trajectory: xtc trr cpt trj gro g96 pdb tng
-n [<.ndx>] (index.ndx) (Input, Optional)
Index file
-o [<.xvg>] (polystat.xvg) (Output)
xvgr/xmgr file
-v [<.xvg>] (polyvec.xvg) (Output, Optional)
xvgr/xmgr file
-p [<.xvg>] (persist.xvg) (Output, Optional)
xvgr/xmgr file
-i [<.xvg>] (intdist.xvg) (Output, Optional)
xvgr/xmgr file
Other options:
-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, 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 ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-polystat(1)
