On Wed, Apr 05, 2006, Don.Bashford.stjude.org 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.
...regards...dave
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Received on Wed Apr 05 2006 - 21:28:16 PDT
