Re: amber-developers: Extra Points Calculation

From: Lachele Foley <>
Date: Tue, 11 Nov 2008 16:23:45 -0500

OK... so... maybe the issue is something like a "vacuum bubble," but I didn't think that happened with minimizations. in fact, I had thought, often to my dismay, that it was not possible to do periodic conditions with a minimization. Have I just been lucky so far and never seen it?

:-) Lachele
B. Lachele Foley, PhD '92,'02
Assistant Research Scientist
Complex Carbohydrate Research Center, UGA
----- Original Message -----
From: Volodymyr Babin
Sent: Tue, 11 Nov
2008 15:35:55 -0500
Subject: Re: amber-developers: Extra Points
> On Tue, November 11, 2008 15:31, Lachele Foley wrote:
> >> These look perfectly fine, i.e., the output does not depend on the
> >> number of cpus, which is good.
> >
> > But, the end result of the minimization, after 14,000 steps, most
> > certainly is not fine.  In fact, it is very bad.  It has a great big gap
> > running down the middle of it.
> >
> > So, my guess about the different processors was wrong... and I don't know
> > enough about the code to make any other guesses.  I have no clue why it
> > would do that, but it does look sort-of as if it divided the waters into
> > two sets and minimized them separately, and the sucrose separately, still.
> Could you send me the files? Is there a slight chance that the outcome
> is indeed "the minimum" (i.e., did the energy go down all the time?)
> Volodymyr
Received on Fri Dec 05 2008 - 14:30:38 PST
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