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

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)^2 + R_i(z)^2))/(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:

Input trajectory or single configuration: xtc trr cpt gro g96 pdb tng
Input structure: tpr gro g96 pdb brk ent
Extra index groups

Options to specify output files:

Filename for gyrate plot output

Other options:

First frame (ps) to read from trajectory
Last frame (ps) to read from trajectory
Only use frame if t MOD dt == first time (ps)
Unit for time values: fs, ps, ns, us, ms, s
Atoms stored in the trajectory file (if not set, assume first N atoms)
Plot formatting: xmgrace, xmgr, none
-[no]rmpbc (yes)
Make molecules whole for each frame
Provide selections from files
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
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
Select group to compute gyrate radius
Atom weighting mode: mass, charge, geometry

SEE ALSO

gmx(1)

More information about GROMACS is available at <http://www.gromacs.org/>.

COPYRIGHT

2024, GROMACS development team

February 28, 2024 2024.1