Re: AMBER: Computing psec/day using Amber 8

From: David A. Case <>
Date: Thu, 6 May 2004 11:42:37 -0700

On Thu, May 06, 2004, Craig TOEPFER wrote:
> On the Amber website, there are some benchmark results from various
> machines/compilers. The results are listed as "ps per day". I am not
> sure how to compute this value from the output produced by these set of
> benchmarks that are included in the Amber8 distribution. Can you help
> me or point me in the right direction.

The fourth "Note" at the top of the benchmark page gives the conversion:

The value of ps per day = 86.4/(seconds per step), for a time step of 1 fs.
Double this value if you plan to use 2 fs time steps.

The "jac" benchmark uses a 1 fs time step, for example, and it is 1000 steps
long. So you figure out your seconds per step, and use the above equation.

....good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
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Received on Thu May 06 2004 - 19:53:01 PDT
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