AMBER Archive (2009)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Nov 25 2009 - 11:10:56 CST

what is the thermostat?

On Wed, Nov 25, 2009 at 12:05 PM, Da-Wei Li <lidawei_at_gmail.com> 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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