1 .TH g_polystat 1 "Thu 16 Oct 2008"
3 g_polystat - calculates static properties of polymers
10 .BI "-n" " index.ndx "
11 .BI "-o" " polystat.xvg "
12 .BI "-v" " polyvec.xvg "
13 .BI "-p" " persist.xvg "
25 g_polystat plots static properties of polymers as a function of time
26 and prints the average.
29 By default it determines the average end-to-end distance and radii
30 of gyration of polymers. It asks for an index group and split this
31 into molecules. The end-to-end distance is then determined using
32 the first and the last atom in the index group for each molecules.
33 For the radius of gyration the total and the three principal components
34 for the average gyration tensor are written.
37 the eigenvectors are written.
40 also the average eigenvalues of the individual
41 gyration tensors are written.
46 the presistence length is determined.
47 The chosen index group should consist of atoms that are
48 consecutively bonded in the polymer mainchains.
49 The presistence length is then determined from the cosine of
50 the angles between bonds with an index difference that is even,
51 the odd pairs are not used, because straight polymer backbones
52 are usually all trans and therefore only every second bond aligns.
53 The persistence length is defined as number of bonds where
54 the average cos reaches a value of 1/e. This point is determined
55 by a linear interpolation of log(cos).
59 Run input file: tpr tpb tpa
63 Trajectory: xtc trr trj gro g96 pdb cpt
69 .BI "-o" " polystat.xvg"
73 .BI "-v" " polyvec.xvg"
77 .BI "-p" " persist.xvg"
83 Print help info and quit
85 .BI "-nice" " int" " 19"
88 .BI "-b" " time" " 0 "
89 First frame (ps) to read from trajectory
91 .BI "-e" " time" " 0 "
92 Last frame (ps) to read from trajectory
94 .BI "-dt" " time" " 0 "
95 Only use frame when t MOD dt = first time (ps)
97 .BI "-tu" " enum" " ps"
113 View output xvg, xpm, eps and pdb files
115 .BI "-[no]xvgr" "yes "
116 Add specific codes (legends etc.) in the output xvg files for the xmgrace program
119 Use the mass weighting for radii of gyration
122 Plot average eigenvalues