How to find radius of gyration of individual polymer chains in gmx

User discussions
1

GROMACS version: 2020.5
GROMACS modification: No

I am running a simulation with multiple polymer chains in a box of solvated with water. I want to check the radius of gyration of each individual polymer chain.

From what I understand, gmx gyrate -s md.tpr -f md.xtc works fine when I have a single molecule in my box. However, if I have multiple polymer chains in my box, how do I track the ROG of each chain over time from gromacs? Is there an in-built functionality to do something of this nature?

2

You need to create an index group that specifies the chain(s) of interest as separate groups and analyze them individually.

3

Got it, thank you for the advice