AMBER Archive (2006)

Subject: Re: AMBER: Restarting constant pressure sims with restraints

From: David A. Case (
Date: Wed Apr 05 2006 - 13:24:38 CDT

On Wed, Apr 05, 2006, wrote:

> I find that attempting restart a constant-pressure MD sim that uses
> harmonic restraints to the refc coordinates blows up.

This is a known bug/limitation. You are fine if the refc coordinates are the
same as the starting coordinates for that particular run, but you can't
continue to use (say) the x-ray coordinates for restarting runs that have been
done using constant pressure.

I generally just have the refc coords be the same as the starting coords for
that particular run. This means that the reference coordinates move a little
bit from the x-ray (say) coords, but generally only by 0.2 -0.4 Angstroms,
which I am willing to live with.

I also try to make my first constant pressure run (where I can still use the
true x-ray coords as refc) be a longish run, so that I get as much
equilibration as possible with the original coordinates as restraints.

But then the scaled refc would no longer be the real original structure;
so it's not clear to me that this is the best answer either. I don't know if
pmemd has some different way to handle this problem or not.

Fixes would be welcomed.


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