restart with constraints causes RMSD "jump"

From: P.-L. Chau (
Date: Wed May 25 2011 - 07:24:11 CDT

I would like to re-ask the question which was posted on the NAMD mailing
list last year:

This question still has not received a reply. I personally emailed the
scientist who posted it and he said that he still had not found an answer.

I note that in a previous publication (Sotomayor and Schulten (2004)
Biophysical Journal, 87, 3050-3065) the authors use constraints in an NPT
ensemble. Their constraints act only on the main-chain atoms. I am running
a similar system where the constraints act on all the protein atoms, but
not on the surrounding hydrated membrane.

I found that on stopping the run and restarting, there was a "jump" in the
r.m.s. deviation, as was reported previously on the NAMD mailing list. It
is well known that r.m.s. deviations fluctuate, but there was an abrupt
increase in the value around which it fluctuated.

If I cancelled the constraints, then this "jump" disappeared. If I
shortened each run to only 200 time-steps, this "jump" also disappeared.
Lastly, if I used a much smaller protein, then even if I put constraints
on the whole protein and run long simulations, this "jump" was not
observed. It appeared that this "jump" came from doing long simulations on
a large system (>330000 atoms) with constraints.

I would like to ask if any of you have met with this problem, and if so,
whether there is any fix for it. I am sorry I have not included any of the
files, graphs and analysis results because they take up too much space. I
shall be happy to email those to anybody who is interested, or put them on
a website so they can be downloaded.

Thank you very much indeed.

P-L Chau

Bioinformatique Structurale
Institut Pasteur
75724 Paris

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