---
name: "gmx-gyrate-legacy"
section: "1"
platform: "linux"
package: "gromacs-data"
version: "2025.2-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/gmx-gyrate-legacy"
---

# gmx-gyrate-legacy(1)

Calculate the radius of gyration

## NAME

gmx-gyrate-legacy - Calculate the radius of gyration

## SYNOPSIS

```
gmx gyrate-legacy [-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-legacy** 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)](/gmx/1.md)**

More information about GROMACS is available at \<*http://www.gromacs.org/*\>.

## COPYRIGHT

2025, GROMACS development team