g_polystat - calculates static properties of polymers
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
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).
-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.
-o polystat.xvg Output
-v polyvec.xvg Output, Opt.
-p persist.xvg Output, Opt.
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
View output xvg, xpm, eps and pdb files
Add specific codes (legends etc.) in the output xvg files for the
Use the mass weighting for radii of gyration
Plot average eigenvalues
More information about GROMACS is available at
Thu 16 Oct 2008 g_polystat(1)