---
name: "g_gyrate_d"
section: "1"
platform: "linux"
package: "gromacs-data"
version: "5.0.2-1"
release: "Debian 8 (Jessie)"
platforms: ["linux"]
url: "https://new.carta.tech/gmx-gyrate"
---

# g\_gyrate\_d(1)

Calculate the radius of gyration

Part of [gmx-gyrate(1)](/gmx-gyrate/1.md).

## NAME

gmx-gyrate - Calculate the radius of gyration

## SYNOPSIS

gmx gyrate \[-f \[\<.xtc/.trr/...\>\]\] \[-s \[\<.tpr/.tpb/...\>\]\]\
            \[-n \[\<.ndx\>\]\] \[-o \[\<.xvg\>\]\] \[-acf \[\<.xvg\>\]\] \[-nice \<int\>\]\
            \[-b \<time\>\] \[-e \<time\>\] \[-dt \<time\>\] \[-\[no\]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.

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 and output files:

**-f** *\[\<.xtc/.trr/...\>\] (traj.xtc) (Input)*\
     Trajectory: xtc trr cpt trj gro g96 pdb tng

**-s** *\[\<.tpr/.tpb/...\>\] (topol.tpr) (Input)*\
     Structure+mass(db): tpr tpb tpa gro g96 pdb brk ent

**-n** *\[\<.ndx\>\] (index.ndx) (Input, Optional)*\
     Index file

**-o** *\[\<.xvg\>\] (gyrate.xvg) (Output)*\
     xvgr/xmgr file

**-acf** *\[\<.xvg\>\] (moi-acf.xvg) (Output, Optional)*\
     xvgr/xmgr file

Other options:

**-nice** *\<int\> (19)*\
     Set the nicelevel

**-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 when t MOD dt = first time (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, vac, exp5, exp7, exp9, erffit

**-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

**[gromacs(7)](/gromacs/7.md)**

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