1GMX-GYRATE(1)                       GROMACS                      GMX-GYRATE(1)
2
3
4

NAME

6       gmx-gyrate - Calculate the radius of gyration
7

SYNOPSIS

9          gmx gyrate [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
10                     [-o [<.xvg>]] [-acf [<.xvg>]] [-b <time>] [-e <time>]
11                     [-dt <time>] [-[no]w] [-xvg <enum>] [-nmol <int>] [-[no]q]
12                     [-[no]p] [-[no]moi] [-nz <int>] [-acflen <int>]
13                     [-[no]normalize] [-P <enum>] [-fitfn <enum>]
14                     [-beginfit <real>] [-endfit <real>]
15

DESCRIPTION

17       gmx  gyrate computes the radius of gyration of a molecule and the radii
18       of gyration about the x-, y- and z-axes, as a  function  of  time.  The
19       atoms are explicitly mass weighted.
20
21       The  axis  components corresponds to the mass-weighted root-mean-square
22       of the radii components orthogonal to each axis, for example:
23
24       Rg(x) = sqrt((sum_i m_i (R_i(y)^2 + R_i(z)^2))/(sum_i m_i)).
25
26       With the -nmol option the radius of gyration  will  be  calculated  for
27       multiple  molecules  by  splitting  the analysis group in equally sized
28       parts.
29
30       With the option -nz 2D radii of gyration in the  x-y  plane  of  slices
31       along the z-axis are calculated.
32

OPTIONS

34       Options to specify input files:
35
36       -f [<.xtc/.trr/…>] (traj.xtc)
37              Trajectory: xtc trr cpt gro g96 pdb tng
38
39       -s [<.tpr/.gro/…>] (topol.tpr)
40              Structure+mass(db): tpr gro g96 pdb brk ent
41
42       -n [<.ndx>] (index.ndx) (Optional)
43              Index file
44
45       Options to specify output files:
46
47       -o [<.xvg>] (gyrate.xvg)
48              xvgr/xmgr file
49
50       -acf [<.xvg>] (moi-acf.xvg) (Optional)
51              xvgr/xmgr file
52
53       Other options:
54
55       -b <time> (0)
56              Time of first frame to read from trajectory (default unit ps)
57
58       -e <time> (0)
59              Time of last frame to read from trajectory (default unit ps)
60
61       -dt <time> (0)
62              Only use frame when t MOD dt = first time (default unit ps)
63
64       -[no]w (no)
65              View output .xvg, .xpm, .eps and .pdb files
66
67       -xvg <enum> (xmgrace)
68              xvg plot formatting: xmgrace, xmgr, none
69
70       -nmol <int> (1)
71              The number of molecules to analyze
72
73       -[no]q (no)
74              Use  absolute value of the charge of an atom as weighting factor
75              instead of mass
76
77       -[no]p (no)
78              Calculate the radii of gyration about the principal axes.
79
80       -[no]moi (no)
81              Calculate the moments  of  inertia  (defined  by  the  principal
82              axes).
83
84       -nz <int> (0)
85              Calculate  the  2D  radii  of  gyration of this number of slices
86              along the z-axis
87
88       -acflen <int> (-1)
89              Length of the ACF, default is half the number of frames
90
91       -[no]normalize (yes)
92              Normalize ACF
93
94       -P <enum> (0)
95              Order of Legendre polynomial for ACF (0 indicates none):  0,  1,
96              2, 3
97
98       -fitfn <enum> (none)
99              Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9
100
101       -beginfit <real> (0)
102              Time where to begin the exponential fit of the correlation func‐
103              tion
104
105       -endfit <real> (-1)
106              Time where to end the exponential fit of the  correlation  func‐
107              tion, -1 is until the end
108

SEE ALSO

110       gmx(1)
111
112       More     information    about    GROMACS    is    available    at    <‐
113       http://www.gromacs.org/>.
114

116       2019, GROMACS development team
117
118
119
120
1212018.7                           May 29, 2019                    GMX-GYRATE(1)
Impressum