Re: amber-developers: amber performance

From: David A. Case <>
Date: Thu, 1 Mar 2007 10:50:34 -0800

On Wed, Feb 28, 2007, Ross Walker wrote:
> Tom C and I spent some time talking about this on Sunday evening. We pretty
> much came to the conclusion that we want to do is design a series of
> calculations that attempt to address the various issues that people simply
> "believe" at present. I.e. find something that is sensitive to single vs
> double precision and see if we can address whether single precision is okay
> or not.

In my view, this could very easily become a time sink where you don't get
any definitive results and just waste time and create controvesy. The way in
which gromacs and desmond use single precision is quite different, and both
would be different from trying to compile sander in single precision.

> In addition we thought about answering PME vs force switch
> simulations. Here a salt water solution simulation might be useful as this
> would be an extreme test of the electrostatics and we could address whether
> a force switch cutoff is actually okay or if you really need pme.

Bob has already answered this, pointing out quite eloquently ways in which
this could become another wild-goose chase. And, since he already has so much
data in this area, starting some new effort here doesn't seem very productive.

> A straight benchmark paper is unlikely to get published so I think wrapping
> it up in a paper that attempts to address issues regarding PME, time step,
> single vs double precision etc is a good way to go.

We don't necessarily need a paper on benchmarks: a good web site that collects
numbers we already have lying around (plus some new calculations) would go a
long way in my view. A key need: someone in the Amber community needs to be
able to run gromacs and namd, so we can do our own side-by-side comparisons.

The usual $.02 disclaimers go here.

Received on Sun Mar 04 2007 - 06:07:43 PST
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