Re: amber-developers: amber performance

From: Robert Duke <>
Date: Wed, 28 Feb 2007 17:58:47 -0500

Scott -
Great! I will be working for a little bit to get tip4p (actually I will
probably just go ahead and do full extra pnts support), remd, ti into a
checked in version of pmemd so the various amber developers can start
reaping the benefits; then I will go back to pushing performance and can
have pieces of that available for "pmemd 10 beta" performance comparison.
Right now, the code base I have is not significantly faster than 9; I have
been spending time on design issues, ff validity, electrostatic methods
validity, etc. But I'll have some of this stuff working hopefully before
too long.
Best Regards - Bob

----- Original Message -----
From: "Scott Brozell" <>
To: <>
Sent: Wednesday, February 28, 2007 5:24 PM
Subject: amber-developers: amber performance

> Hi,
> Today Kent Milfeld from TACC asked me about amber performance because
> he saw that there is work underway for charmm's performance.
> I told him about pmemd (which he had never heard of), namd, gromacs, etc.
> He was very receptive to the idea that namd has great advertising
> and might not be targeting the best science.
> This follows on the discussion we had at the amber meeting regarding
> a publication on good vs dubious science, pmemd, single vs double
> precision,
> scaling vs throughput, etc. I hope that the ball will be rolling soon.
> And I'm happy to help out.
> Scott
Received on Sun Mar 04 2007 - 06:07:26 PST
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