Re: amber-developers: Extra Points Calculation

From: Lachele Foley <lfoley.ccrc.uga.edu>
Date: Tue, 11 Nov 2008 09:41:12 -0500

> understand the exact storage requirement, and get data organized in such a
> manner as to increase cache utilization

Yes. Good idea. Of course. I'm all for efficient resource use. I was wondering how hard it would be to implement a dynamic sort of allocation in this situation. Seems it ought to be possible, but my last significant fortran was back in... oh... 1987, and there wasn't much of it even then.

> but if someone wants to shoot me a
> copy of the runfiles, I will see what it does in pmemd.

Will do, in just a moment.

:-) 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: Robert Duke
[mailto:rduke.email.unc.edu]
To: amber-developers.scripps.edu
Sent: Tue, 11
Nov 2008 08:50:49 -0500
Subject: Re: amber-developers: Extra Points
Calculation
[snip]
> 
> ----- Original Message ----- 
> From: "David A. Case" <case.biomaps.rutgers.edu>
> To: <amber-developers.scripps.edu>
> Sent: Tuesday, November 11, 2008 7:08 AM
> Subject: Re: amber-developers: Extra Points Calculation
> 
> 
> > On Mon, Nov 10, 2008, Volodymyr Babin wrote:
> >>
> >> please see the patch for cvs sander attached. Does it
> >> look harmless enough to be committed?
> >
> > Does it solve Lachele's problem (the sucrose_EP test case)?  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 tried to expand the size of max14 (not as much as you did), and was 
> > still
> > getting segfaults on Lachele's example.  But it is great if your fix 
> > works.
> >
> > ...dac
> >
> > 
> 
> 

Received on Fri Dec 05 2008 - 14:25:53 PST