Main Table of Contents

Wed 13 Nov 2013


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>).


-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]h bool no Print help info and quit
-[no]version bool no 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]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]mw bool yes Use the mass weighting for radii of gyration
-[no]pc bool no Plot average eigenvalues