AMBER Archive (2009)

Subject: Re: [AMBER] how to know that adequate equilibration from rmsd curve of equilibration

From: Carlos Simmerling (
Date: Thu May 28 2009 - 13:15:09 CDT

that's way too general. it depends on many things, such as the quality of
the experimental structure, the difference in conditions between your
simulation and the experiment (pH, solvent, ions etc) and where in the
structure the rmsd values come from. rmsd is a very broad measure and a
value of 2 may mean that all regions differ by about 2, or that many differ
by 1 and others differ by a larger number (for example 5, or maybe 10). rmsd
itself is only 1 measure of simulation quality so I strongly disagree that
simulation rmsd values should "not be greater than 2". if you do get larger
values, though, you should find out why and see if there is a way to
validate that the behavior is reasonable.

equilibration can be very tricky and there is no one "correct" protocol we
can give. it depends again on the initial structure and any differences in
your simulation conditions from the expt. it is entirely possible to have
most of the structure look ok, but due to bad placement of an H atom or even
an ion, part of the initial structure will be incorrectly modeled and the
simulation will not give a good model. equilibration can help with these but
you need detailed information about differences between MD and experiment to
proceed. we tend to be cautious and use about 10 steps in our general
equilibration procedure, and more when anything was modeled (such as a side
chain or a ligand).

On Thu, May 28, 2009 at 2:08 PM, nicholus bhattacharjee <> wrote:

> Thank you Bill. But you did not answer my second question. Is the rmsd
> value
> between the initial structure and the final structure be not more than 2
> Armstrong.
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