1 .TH g_polystat 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
3 g_polystat - calculates static properties of polymers
8 .BI "\-s" " topol.tpr "
10 .BI "\-n" " index.ndx "
11 .BI "\-o" " polystat.xvg "
12 .BI "\-v" " polyvec.xvg "
13 .BI "\-p" " persist.xvg "
14 .BI "\-i" " intdist.xvg "
16 .BI "\-[no]version" ""
27 \&g_polystat plots static properties of polymers as a function of time
28 \&and prints the average.
31 \&By default it determines the average end\-to\-end distance and radii
32 \&of gyration of polymers. It asks for an index group and split this
33 \&into molecules. The end\-to\-end distance is then determined using
34 \&the first and the last atom in the index group for each molecules.
35 \&For the radius of gyration the total and the three principal components
36 \&for the average gyration tensor are written.
37 \&With option \fB \-v\fR the eigenvectors are written.
38 \&With option \fB \-pc\fR also the average eigenvalues of the individual
39 \&gyration tensors are written.
40 \&With option \fB \-i\fR the mean square internal distances are
44 \&With option \fB \-p\fR the persistence length is determined.
45 \&The chosen index group should consist of atoms that are
46 \&consecutively bonded in the polymer mainchains.
47 \&The persistence length is then determined from the cosine of
48 \&the angles between bonds with an index difference that is even,
49 \&the odd pairs are not used, because straight polymer backbones
50 \&are usually all trans and therefore only every second bond aligns.
51 \&The persistence length is defined as number of bonds where
52 \&the average cos reaches a value of 1/e. This point is determined
53 \&by a linear interpolation of log(cos).
55 .BI "\-s" " topol.tpr"
57 Run input file: tpr tpb tpa
61 Trajectory: xtc trr trj gro g96 pdb cpt
63 .BI "\-n" " index.ndx"
67 .BI "\-o" " polystat.xvg"
71 .BI "\-v" " polyvec.xvg"
75 .BI "\-p" " persist.xvg"
79 .BI "\-i" " intdist.xvg"
85 Print help info and quit
87 .BI "\-[no]version" "no "
88 Print version info and quit
90 .BI "\-nice" " int" " 19"
93 .BI "\-b" " time" " 0 "
94 First frame (ps) to read from trajectory
96 .BI "\-e" " time" " 0 "
97 Last frame (ps) to read from trajectory
99 .BI "\-dt" " time" " 0 "
100 Only use frame when t MOD dt = first time (ps)
102 .BI "\-tu" " enum" " ps"
103 Time unit: \fB fs\fR, \fB ps\fR, \fB ns\fR, \fB us\fR, \fB ms\fR or \fB s\fR
106 View output xvg, xpm, eps and pdb files
108 .BI "\-xvg" " enum" " xmgrace"
109 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR
111 .BI "\-[no]mw" "yes "
112 Use the mass weighting for radii of gyration
115 Plot average eigenvalues
120 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.