Scroll to navigation

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

NAME

gmx-gyrate - Calculate the radius of gyration

SYNOPSIS

gmx gyrate [ -f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
           [ -o [<.xvg>]] [-acf [<.xvg>]] [-b <time>] [-e <time>]
           [ -dt <time>] [-[no]w] [-xvg <enum>] [-nmol <int>] [-[no]q]
           [ -[no]p] [-[no]moi] [-nz <int>] [-acflen <int>]
           [ -[no]normalize] [-P <enum>] [-fitfn <enum>]
           [ -beginfit <real>] [-endfit <real>]


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 m_i (R_i(y)^2 + R_i(z)^2))/(sum_i m_i)).
With the -nmol option the radius of gyration will be calculated for multiple molecules by splitting the analysis group in equally sized parts.
With the option -nz 2D radii of gyration in the x-y plane of slices along the z-axis are calculated.

OPTIONS

Options to specify input files:
-f [<.xtc/.trr/…>] (traj.xtc)
Trajectory: xtc trr cpt gro g96 pdb tng
-s [<.tpr/.gro/…>] (topol.tpr)
Structure+mass(db): tpr gro g96 pdb brk ent
-n [<.ndx>] (index.ndx) (Optional)
Index file

Options to specify output files:
-o [<.xvg>] (gyrate.xvg)
xvgr/xmgr file
-acf [<.xvg>] (moi-acf.xvg) (Optional)
xvgr/xmgr file

Other options:
-b <time> (0)
Time of first frame to read from trajectory (default unit ps)
-e <time> (0)
Time of last frame to read from trajectory (default unit ps)
-dt <time> (0)
Only use frame when t MOD dt = first time (default unit ps)
-[no]w (no)
View output .xvg, .xpm, .eps and .pdb files
-xvg <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, none
-nmol <int> (1)
The number of molecules to analyze
-[no]q (no)
Use absolute value of the charge of an atom as weighting factor instead of mass
-[no]p (no)
Calculate the radii of gyration about the principal axes.
-[no]moi (no)
Calculate the moments of inertia (defined by the principal axes).
-nz <int> (0)
Calculate the 2D radii of gyration of this number of slices along the z-axis
-acflen <int> (-1)
Length of the ACF, default is half the number of frames
-[no]normalize (yes)
Normalize ACF
-P <enum> (0)
Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2, 3
-fitfn <enum> (none)
Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9
-beginfit <real> (0)
Time where to begin the exponential fit of the correlation function
-endfit <real> (-1)
Time where to end the exponential fit of the correlation function, -1 is until the end

SEE ALSO

gmx(1)
More information about GROMACS is available at < http://www.gromacs.org/>.

COPYRIGHT

2018, GROMACS development team
June 14, 2018 2018.2