1GMX-POLYSTAT(1)                     GROMACS                    GMX-POLYSTAT(1)
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NAME

6       gmx-polystat - Calculate static properties of polymers
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SYNOPSIS

9          gmx polystat [-s [<.tpr>]] [-f [<.xtc/.trr/...>]] [-n [<.ndx>]]
10                       [-o [<.xvg>]] [-v [<.xvg>]] [-p [<.xvg>]] [-i [<.xvg>]]
11                       [-b <time>] [-e <time>] [-dt <time>] [-tu <enum>]
12                       [-[no]w] [-xvg <enum>] [-[no]mw] [-[no]pc]
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DESCRIPTION

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

39       Options to specify input files:
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41       -s [<.tpr>] (topol.tpr)
42              Portable xdr run input file
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44       -f [<.xtc/.trr/…>] (traj.xtc)
45              Trajectory: xtc trr cpt gro g96 pdb tng
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47       -n [<.ndx>] (index.ndx) (Optional)
48              Index file
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50       Options to specify output files:
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52       -o [<.xvg>] (polystat.xvg)
53              xvgr/xmgr file
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55       -v [<.xvg>] (polyvec.xvg) (Optional)
56              xvgr/xmgr file
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58       -p [<.xvg>] (persist.xvg) (Optional)
59              xvgr/xmgr file
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61       -i [<.xvg>] (intdist.xvg) (Optional)
62              xvgr/xmgr file
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64       Other options:
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66       -b <time> (0)
67              Time of first frame to read from trajectory (default unit ps)
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69       -e <time> (0)
70              Time of last frame to read from trajectory (default unit ps)
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72       -dt <time> (0)
73              Only use frame when t MOD dt = first time (default unit ps)
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75       -tu <enum> (ps)
76              Unit for time values: fs, ps, ns, us, ms, s
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78       -[no]w (no)
79              View output .xvg, .xpm, .eps and .pdb files
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81       -xvg <enum> (xmgrace)
82              xvg plot formatting: xmgrace, xmgr, none
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84       -[no]mw (yes)
85              Use the mass weighting for radii of gyration
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87       -[no]pc (no)
88              Plot average eigenvalues
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SEE ALSO

91       gmx(1)
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93       More    information    about    GROMACS    is    available    at     <‐
94       http://www.gromacs.org/>.
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97       2020, GROMACS development team
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1022019.6                           Feb 28, 2020                  GMX-POLYSTAT(1)
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