Re: amber-developers: Extra Points Calculation

From: Lachele Foley <>
Date: Tue, 11 Nov 2008 13:27:09 -0500

> We thought it does, but Lachele discovered more problems yesterday
> evening; he was going to take a look today.

I kept having jobs fail... I could only get them to behave on 2 processors. I hadn't even looked, graphically, at the output. Silly me.

The minimization isn't doing quite what I expect. Load the attached topology and restart into vmd or something and you will find, if you twirl the system the right way, a lovely rift between two halves of the solvent, with the sucrose molecule spanning the gap, more or less. The starting coordinates look like a standard array of water molecules dropped around a solvent, so this is something the minimization is doing. Also attached is my file in case there is some EP-relevant keyword I didn't set properly. If I had to make a blind guess, I'd say the two processors aren't talking to each other in quite the way they should -- like half the solvent went to one, and half went to the other, and neither knows exactly where the other is. Or something.

And, for what it's worth, The CP running on two processors seems to be slowly correcting the problem. It's over 100,000 steps and the coordinates look pretty good now. At first, it was what you'd expect. I can send some or all of that output if anyone wants to see 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 07:20:07 -0500
Subject: Re: amber-developers: Extra Points
> > Does it solve Lachele's problem (the sucrose_EP test case)?
> We thought it does, but Lachele discovered more problems yesterday
> evening; he was going to take a look today.
> > As far as I can see, that example does not include any "LP" atoms,
> > and I don't think we should be expanding to recollection
> > was that "LP" atoms (still found in
> > some old parameter/topology files) were *not* treated as extra points, but
> > as real atoms.
> I see. Then probably the 'LP  ' part is unneeded indeed. I am not a
> right person to judge here.
> > I tried to expand the size of max14 (not as much as you did), and was
> > still getting segfaults on Lachele's example.
> This is because of too short nb14_list and i14 (their sizes are proportional
> to the max14, but max14 is not used in the corresponding allocate()).
> Volodymyr

Received on Fri Dec 05 2008 - 14:28:15 PST
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