AMBER Archive (2006)

Subject: Re: AMBER: paralelization and sander problems

From: David A. Case (case_at_scripps.edu)
Date: Tue Feb 14 2006 - 10:32:59 CST

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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