1GMX-GYRATE(1)                       GROMACS                      GMX-GYRATE(1)
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NAME

6       gmx-gyrate - Calculate the radius of gyration
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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>]
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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.
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21       The  axis  components corresponds to the mass-weighted root-mean-square
22       of the radii components orthogonal to each axis, for example:
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24       Rg(x) = sqrt((sum_i m_i (R_i(y)^2 + R_i(z)^2))/(sum_i m_i)).
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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.
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30       With the option -nz 2D radii of gyration in the  x-y  plane  of  slices
31       along the z-axis are calculated.
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OPTIONS

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

110       gmx(1)
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112       More     information    about    GROMACS    is    available    at    <‐
113       http://www.gromacs.org/>.
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116       2022, GROMACS development team
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1212022.2                           Jun 16, 2022                    GMX-GYRATE(1)
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