gmx gyrate#

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:

-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