AMBER Archive (2006)

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

From: Robert Duke (rduke_at_email.unc.edu)
Date: Wed Apr 05 2006 - 13:30:05 CDT

In matters like this, pmemd pretty much does exactly what sander does. -
Regards - Bob Duke
----- Original Message -----
From: "David A. Case" <case_at_scripps.edu>
To: <amber_at_scripps.edu>
Sent: Wednesday, April 05, 2006 2:24 PM
Subject: Re: AMBER: Restarting constant pressure sims with restraints

> On Wed, Apr 05, 2006, Don.Bashford_at_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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