GROMACS Tips and Tricks: How to Change the Time in Gyration Plot to ns in GROMACS

One of the most common analyses performed on molecular dynamics trajectories is the calculation of the radius of gyration (Rg). The Rg is a measure of the compactness of a protein and can be used to monitor the folding and unfolding of a protein over time.

In GROMACS, the gmx gyrate tool can be used to calculate the Rg of a protein from a molecular dynamics trajectory.

By default, the gmx gyrate tool outputs the time in picoseconds (ps). However, it is often more convenient to have the time in nanoseconds (ns) for plotting and analysis.

To change the time in gyration plot to ns in GROMACS, you can use the gmx trjconv tool to convert the trajectory to a new format with the time in ns. Here are the steps to change the time in gyration plot to ns:

Use the gmx trjconv tool to convert the trajectory to a new format with the time in ns. For example, to convert the trajectory file traj.xtc to a new format with the time in ns, run the following command:
 gmx trjconv -s topol.tpr -f traj.xtc -o traj_ns.xtc -t0 0 -tu ns

Use the gmx gyrate tool to calculate the Rg of the protein from the new trajectory file with the time in ns. For example, to calculate the Rg of the protein from the new trajectory file traj_ns.xtc, run the following command:
 gmx gyrate -s topol.tpr -f traj_ns.xtc -o gyrate.xvg

Plot the Rg as a function of time using your favorite plotting software.
Please note that the -t0 option in the gmx trjconv command specifies the starting time for the new trajectory file. In this example, we set the starting time to 0 ns. The -tu option specifies the time unit for the new trajectory file. In this example, we set the time unit to ns.

Tags: radius of gyration , GROMACS