# gmx-gyrate man page

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)

-[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