AMBER Archive (2009)

Subject: [AMBER] Re: Verlet update time in explicit water Replica Exchange MD

From: Da-Wei Li (
Date: Wed Nov 25 2009 - 11:12:23 CST

Just provide more information. This strange thing does not happen if
all processors are in one node.


On Wed, Nov 25, 2009 at 12:05 PM, Da-Wei Li <> wrote:
> Dear All:
> I recently try explicit water replica exchange MD using Amber9. The md
> run is very slow, compared with normal constant T runs. A close look
> at the profile_mpi reveals that "Verlet update time" take about 3/4 of
> the CPU times at processor 0. This is not normal. This does not happen
> with constant T MD. I use CentOS and mvapich2.
> Anyone has some idea?
> best,
> dawei

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