Is it norm with RMSD stabilizing at ~1.1 nm when finishing production mdrun?

User discussions
1

GROMACS version: 2021.1
GROMACS modification: No
Hello,
After finishing 300-ns production mdrun, the RMSD (ref: equilibrated) stabilizing at ~ 1.1 nm as shown below:
rmsd_1.1nm_MUT_2021-03-28_095621

Is 1.1 nm is a normal range for my mutated protein? When I search the RMSD range in google and find that mostly the RMSD is less than 1 nm, so I am not sure if my RMSD is OK to use?

Also, for comparison, the wilde-type protein give the RMSD of ~ 0.8 nm, and the shape of “down direct half-circle” looks a little wired for me (I expect it to be stable). Also, at the end time of the simulation, the RMSD falls down suddenly to ~0.6 nm. Do you give some suggestions about this figure? Is it normal to use following structural analysis? Or I need more time to do simulation (but I think 300-ns is already long enough)?

rmsd_0.8 nm_WT_2021-03-28_100834

Thanks,
Ming

2

RMSD is an extrinsic property so there are no rules about what it should be. If you have flexible regions or termini, the value can be artificially inflated.

Bottom line: RMSD tells you very little, if anything, that is useful.

Analyze other structural quantities of interest to see if they are sufficiently converged.

3

Thanks, Justin. Sure, my protein has a flexible CTD. I will check other metrics.
Best,
Ming