From: 김민재 (
Date: Mon Oct 21 2019 - 10:53:46 CDT

Hi everyone,

I made some RMSD plots for an enzyme (1ca2; carbonic anhydrase) that I
equilibriated using NAMD. I'va attached a screenshot of two RMSD plots: the
left had a selection of 'all' while the right has a selection of 'protein.'
Both were aligned and the 'noh' option was chosen. The 'all' selection gave
me a very smooth RMSD curve, which was what I was expecting while the
'protein' selection gave me a much "bumpier" sort of curve.

Could anyone please explain why this may be? Why would adding waters to the
selection smoothen out the RMSD curve? And does this indicate something
wrong went on in the equilibriation run?

Min Jae Kim