NAME
g_polystat - calculates static properties of polymers
VERSION 4.0.1
SYNOPSIS
g_polystat -s topol.tpr -f traj.xtc -n index.ndx -o polystat.xvg -v
polyvec.xvg -p persist.xvg -[no]h -nice int -b time -e time -dt time
-tu enum -[no]w -[no]xvgr -[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 -p the presistence length is determined. The chosen index
group should consist of atoms that are consecutively bonded in the
polymer mainchains. The presistence 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
OTHER OPTIONS
-[no]hno
Print help 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: ps, fs, ns, us, ms or s
-[no]wno
View output xvg, xpm, eps and pdb files
-[no]xvgryes
Add specific codes (legends etc.) in the output xvg files for the
xmgrace program
-[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/>.
Thu 16 Oct 2008 g_polystat(1)