Re: AMBER: Any experience on Dell two quad core system?

From: Andreas Svrcek-Seiler <>
Date: Mon, 13 Aug 2007 19:21:39 +0200 (CEST)

> Thanks for the info. Just to make sure I have this right, this is
> for NAB molecular dynamics, not AMBER, correct?
...yes, but the most important features of AMBER/sander with respect to
implicit solvent are available in NAB, too. So, given the same options,
both should give equally "valid" trajectories.

> Is this the regular 5.1.2 version of NAB? I had forgotten that
> NAB MD was parallelized, I guess.
...I tested the cvs version from July 16 (and right now ver. 5.1.2, since
you asked -> same scaling behavior).

> Wonder why the simulation engine in NAB seemingly parallelizes a
> little better than AMBER?
...NAB (as I tested it) uses openmp parallelization, which is intended for
SMP machines. So one might expect this scales better than MPI on
such a machine (though I know hardly anything about the latter, and did my
first 'mpirun' only today). Besides, I used the newest intel compiler
(10.0.025), which might also have helped(?).

good luck,
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Received on Wed Aug 15 2007 - 06:07:29 PDT
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