NAME¶
g_polystat - calculates static properties of polymers
VERSION 4.5.4-dev-20110404-bc5695c
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/>.