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:

       -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

       2024, GROMACS development team

2024.2                                            May 10, 2024                                     GMX-GYRATE(1)