gmx-gyrate1
Calculate radius of gyration of a molecule
Usage
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>]
Overview
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
Releases
6 releases since Debian 8 (Jessie); the text changed 5 times.
-fgroup since Debian 13 (Trixie);
-sel since Debian 13 (Trixie);
-sf since Debian 13 (Trixie).