Man page - gmx-gyrate-legacy(1)
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apt-get install gromacs-data
Manual
GMX-GYRATE-LEGACY
NAMESYNOPSIS
DESCRIPTION
OPTIONS
SEE ALSO
COPYRIGHT
NAME
gmx-gyrate-legacy - Calculate the radius of gyration
SYNOPSIS
gmx
gyrate-legacy [
-f
[<.xtc/.trr/...>]
]
[
-s
[<.tpr/.gro/...>]
]
[
-n
[<.ndx>]
] [
-o
[<.xvg>]
] [
-acf
[<.xvg>]
]
[
-b
<time>
]
[
-e
<time>
] [
-dt
<time>
] [
-[no]w
] [
-xvg
<enum>
]
[
-nmol
<int>
] [
-[no]q
]
[
-[no]p
] [
-[no]moi
] [
-nz
<int>
]
[
-acflen
<int>
] [
-[no]normalize
]
[
-P
<enum>
]
[
-fitfn
<enum>
] [
-beginfit
<real>
] [
-endfit
<real>
]
DESCRIPTION
gmx gyrate-legacy computes the radius of gyration of a molecule and the radii of gyration about the x -, y - and z -axes, as a function of time. The atoms are explicitly mass weighted.
The axis components corresponds to the mass-weighted root-mean-square of the radii components orthogonal to each axis, for example:
Rg(x) = sqrt((sum_i m_i (R_i(y)ˆ2 + R_i(z)ˆ2))/(sum_i m_i)).
With the -nmol option the radius of gyration will be calculated for multiple molecules by splitting the analysis group in equally sized parts.
With the option -nz 2D radii of gyration in the x-y plane of slices along the z -axis are calculated.
OPTIONS
Options to
specify input files:
-f [<.xtc/.trr/...>] (traj.xtc)
Trajectory: xtc trr cpt gro g96 pdb tng
-s [<.tpr/.gro/...>] (topol.tpr)
Structure+mass(db): tpr gro g96 pdb brk ent
-n [<.ndx>] (index.ndx) (Optional)
Index file
Options to
specify output files:
-o [<.xvg>] (gyrate.xvg)
xvgr/xmgr file
-acf [<.xvg>] (moi-acf.xvg) (Optional)
xvgr/xmgr file
Other options:
-b <time> (0)
Time of first frame to read from trajectory (default unit ps)
-e <time> (0)
Time of last frame to read from trajectory (default unit ps)
-dt <time> (0)
Only use frame when t MOD dt = first time (default unit ps)
-[no]w (no)
View output .xvg , .xpm , .eps and .pdb files
-xvg <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, none
-nmol <int> (1)
The number of molecules to analyze
-[no]q (no)
Use absolute value of the charge of an atom as weighting factor instead of mass
-[no]p (no)
Calculate the radii of gyration about the principal axes.
-[no]moi (no)
Calculate the moments of inertia (defined by the principal axes).
-nz <int> (0)
Calculate the 2D radii of gyration of this number of slices along the z-axis
-acflen <int> (-1)
Length of the ACF, default is half the number of frames
-[no]normalize (yes)
Normalize ACF
-P <enum> (0)
Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2, 3
-fitfn <enum> (none)
Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9
-beginfit <real> (0)
Time where to begin the exponential fit of the correlation function
-endfit <real> (-1)
Time where to end the exponential fit of the correlation function, -1 is until the end
SEE ALSO
gmx(1)
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COPYRIGHT
2025, GROMACS development team