Re: [Fwd: increasing RMSD after 2 ns minimization-equilibration]

From: Mark Abraham (
Date: Wed Feb 08 2006 - 19:14:08 CST

> Hello,
> I'm having a problem minimizing and equilibrating my protein. It's fully solvated (total of 28,000 atoms). RMSD analysis after ~1.5
ns shows that the protein is reaching a plateau, however, as the
equilibrating continues after a total of 2 ns the RMSD begins increasing
from approximately 1.5 Angstroms to almost 3 Angstroms! I'm not sure
what's going on.

Have you tried looking at the trajectory?
> I've used the same parameters, PME grid sizes, etc. when restarting
the run. How long does it usually take for a protein to reach
equilibration? I'm attaching a restart configuration file.

How long is a piece of string? This is totally system dependent. For
initial equilibration, position restraints on the solute can be a good
idea to get the system relaxed without perturbing the starting
configuration, followed by a further equilibration period without such


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