1g_polystat(1)             GROMACS suite, VERSION 4.5             g_polystat(1)
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NAME

6       g_polystat - calculates static properties of polymers
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8       VERSION 4.5
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SYNOPSIS

11       g_polystat  -s  topol.tpr  -f  traj.xtc -n index.ndx -o polystat.xvg -v
12       polyvec.xvg -p persist.xvg -i intdist.xvg -[no]h -[no]version -nice int
13       -b time -e time -dt time -tu enum -[no]w -xvg enum -[no]mw -[no]pc
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DESCRIPTION

16       g_polystat  plots  static  properties of polymers as a function of time
17       and prints the average.
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20       By default it determines the average end-to-end distance and  radii  of
21       gyration  of  polymers.  It asks for an index group and split this into
22       molecules. The end-to-end distance is then determined using  the  first
23       and  the  last  atom  in  the  index group for each molecules.  For the
24       radius of gyration the total and the three principal components for the
25       average  gyration tensor are written.  With option  -v the eigenvectors
26       are written.  With option  -pc also  the  average  eigenvalues  of  the
27       individual  gyration  tensors  are  written.   With option  -i the mean
28       square internal distances are written.
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31       With option  -p the persistence length is determined.  The chosen index
32       group  should  consist  of  atoms  that are consecutively bonded in the
33       polymer mainchains.  The persistence length is then determined from the
34       cosine  of  the  angles  between bonds with an index difference that is
35       even, the odd pairs are not used, because  straight  polymer  backbones
36       are usually all trans and therefore only every second bond aligns.  The
37       persistence length is defined as number of bonds where the average  cos
38       reaches a value of 1/e. This point is determined by a linear interpola‐
39       tion of log(cos).
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FILES

42       -s topol.tpr Input
43        Run input file: tpr tpb tpa
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45       -f traj.xtc Input
46        Trajectory: xtc trr trj gro g96 pdb cpt
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48       -n index.ndx Input, Opt.
49        Index file
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51       -o polystat.xvg Output
52        xvgr/xmgr file
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54       -v polyvec.xvg Output, Opt.
55        xvgr/xmgr file
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57       -p persist.xvg Output, Opt.
58        xvgr/xmgr file
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60       -i intdist.xvg Output, Opt.
61        xvgr/xmgr file
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OTHER OPTIONS

65       -[no]hno
66        Print help info and quit
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68       -[no]versionno
69        Print version info and quit
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71       -nice int 19
72        Set the nicelevel
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74       -b time 0
75        First frame (ps) to read from trajectory
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77       -e time 0
78        Last frame (ps) to read from trajectory
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80       -dt time 0
81        Only use frame when t MOD dt = first time (ps)
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83       -tu enum ps
84        Time unit:  fs,  ps,  ns,  us,  ms or  s
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86       -[no]wno
87        View output xvg, xpm, eps and pdb files
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89       -xvg enum xmgrace
90        xvg plot formatting:  xmgrace,  xmgr or  none
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92       -[no]mwyes
93        Use the mass weighting for radii of gyration
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95       -[no]pcno
96        Plot average eigenvalues
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SEE ALSO

100       gromacs(7)
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102       More  information  about  GROMACS  is  available  at   <http://www.gro‐
103       macs.org/>.
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107                                Thu 26 Aug 2010                  g_polystat(1)