How to calculate the gyration with protein centered

User discussions
1

GROMACS version: 2019.4
GROMACS modification: Yes/No

Dear GROMACS users

I have simulated the complex with one protein and one ligand.
Because I wanted to calculate the radius of gyration with the protein centered,
I read the Cmmand-line reference, and there is option -nmol

So, I issued the command line below and select the Group 1(Protein):

gmx_mpi gyrate -s MD/md10ns.tpr -f MD/md10ns_mol.xtc -n /INDEX/index.ndx -o MD/md10ns_gyrate_test.xvg -nmol 1

Is it right for the my purpose?

Thanks.

2

-nmol 1 is the default behavior so there is no need to specify it.

3

Thank you for your reply :)