AMBER Archive (2004)

Subject: Re: AMBER: Computing psec/day using Amber 8

From: David A. Case (
Date: Thu May 06 2004 - 13:42:37 CDT

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 | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to