Re: AMBER: paralelization and sander problems

From: David A. Case <>
Date: Tue, 14 Feb 2006 08:32:59 -0800

On Tue, Feb 14, 2006, Carlos Simmerling wrote:

> in the third MD step (of ~1fs each) or third time that the
> energy is written in the output (which could be longer)?
> I get identical output for different # of cpus up to a few hundred
> steps of 1fs each.

Note that this is expected to be true for a well-equilibrated structure. If
you have bad initial forces, then the round-off error (and hence, the
difference between different numbers of cpus), can be much bigger.

If you are concerned, try the same test with pmemd rather than sander.

...good luck...dac

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Received on Sun Feb 19 2006 - 06:10:11 PST
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