Man page - gmx-gyrate(1)
Packages contains this manual
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apt-get install gromacs-data
Manual
GMX-GYRATE
NAMESYNOPSIS
DESCRIPTION
OPTIONS
SEE ALSO
COPYRIGHT
NAME
gmx-gyrate - Calculate radius of gyration of a molecule
SYNOPSIS
gmx gyrate
[
-f
[<.xtc/.trr/...>]
] [
-s
[<.tpr/.gro/...>]
] [
-n
[<.ndx>]
]
[
-o
[<.xvg>]
] [
-b
<time>
] [
-e
<time>
]
[
-dt
<time>
]
[
-tu
<enum>
] [
-fgroup
<selection>
] [
-xvg
<enum>
]
[
-[no]rmpbc
] [
-sf
<file>
]
[
-selrpos
<enum>
]
[
-seltype
<enum>
] [
-sel
<selection>
] [
-mode
<enum>
]
DESCRIPTION
gmx gyrate 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 w_i (R_i(y)ˆ2 + R_i(z)ˆ2))/(sum_i w_i)).
where w_i is the weight value in the given situation (mass, charge, unit)
Note that this is a new implementation of the gyrate utility added in GROMACS 2024. If you need the old one, use gmx gyrate-legacy .
OPTIONS
Options to
specify input files:
-f [<.xtc/.trr/...>] (traj.xtc) (Optional)
Input trajectory or single configuration: xtc trr cpt gro g96 pdb tng
-s [<.tpr/.gro/...>] (topol.tpr) (Optional)
Input structure: tpr gro g96 pdb brk ent
-n [<.ndx>] (index.ndx) (Optional)
Extra index groups
Options to
specify output files:
-o [<.xvg>] (gyrate-taf.xvg)
Filename for gyrate plot output
Other options:
-b <time> (0)
First frame (ps) to read from trajectory
-e <time> (0)
Last frame (ps) to read from trajectory
-dt <time> (0)
Only use frame if t MOD dt == first time (ps)
-tu <enum> (ps)
Unit for time values: fs, ps, ns, us, ms, s
-fgroup <selection>
Atoms stored in the trajectory file (if not set, assume first N atoms)
-xvg <enum> (xmgrace)
Plot formatting: xmgrace, xmgr, none
-[no]rmpbc (yes)
Make molecules whole for each frame
-sf <file>
Provide selections from files
-selrpos <enum> (atom)
Selection reference positions: atom, res_com, res_cog, mol_com, mol_cog, whole_res_com, whole_res_cog, whole_mol_com, whole_mol_cog, part_res_com, part_res_cog, part_mol_com, part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog
-seltype <enum> (atom)
Default selection output positions: atom, res_com, res_cog, mol_com, mol_cog, whole_res_com, whole_res_cog, whole_mol_com, whole_mol_cog, part_res_com, part_res_cog, part_mol_com, part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog
-sel <selection>
Select group to compute gyrate radius
-mode <enum> (mass)
Atom weighting mode: mass, charge, geometry
SEE ALSO
gmx(1)
More information about GROMACS is available at <- http://www.gromacs.org/ >.
COPYRIGHT
2025, GROMACS development team