Re: amber-developers: Extra Points Calculation

From: Lachele Foley <lfoley.ccrc.uga.edu>
Date: Tue, 11 Nov 2008 13:33:09 -0500

PS to the previous... the minimization was run on four processors... Sorry for any confusion.


:-) Lachele
--
B. Lachele Foley, PhD '92,'02
Assistant Research Scientist
Complex Carbohydrate Research Center, UGA
706-542-0263
lfoley.ccrc.uga.edu
----- Original Message -----
From: Lachele Foley
[mailto:lfoley.ccrc.uga.edu]
To: amber-developers.scripps.edu
Sent: Tue, 11
Nov 2008 13:27:09 -0500
Subject: Re: amber-developers: Extra Points
Calculation
> > 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 MIN.in 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
> 706-542-0263
> lfoley.ccrc.uga.edu
> 
> 
> ----- Original Message -----
> From: Volodymyr Babin
> [mailto:vbabin.ncsu.edu]
> To: amber-developers.scripps.edu
> Sent: Tue, 11 Nov
> 2008 07:20:07 -0500
> Subject: Re: amber-developers: Extra Points
> Calculation
> 
> 
> > > 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 that...my 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 - 14:28:29 PST
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