Radius of Gyration (R_g)

Introduction

Radius of Gyration (R_g) is a measure of protein size and compactness across the duration of the simulation. Fluctuations in R_g can also indicate protein flexibility and stability, where dramatic increases in R_g may suggest unfolding or expansion. R_g can be calculated using gmx gyrate and is generally reported as nanometers (nm) plotted against time.

R_g graph from one set of simulations. R_g is plotted as nanometer (nm) versus time (ns).

You should have the following files:

• Trajectory files (.xtc)
• Topology file (.tpr)

Note

gmx gyrate was changed in the 2024 version of GROMACS. This page references the command as it was in prior releases.

Using gmx gyrate

To calculate radius of gyration:

gmx gyrate -f trajectory.xtc -s topology.tpr -o gyrate.xvg

Other options you may find useful

• -n: index file to be used (see Creating Index Files)
• -b and -e: the frames to begin and end

When prompted, select the group you want to analyze. This will likely be Backbone or another special group, like for individual chains. Note that special groups will require a custom index file to be supplied with -n.

This will output an XVG file of R_g versus time that can be visualized using Grace or Python.

Additional Resources

• gmx gyrate