AMBER Archive (2009)

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

From: Da-Wei Li (lidawei_at_gmail.com)
Date: Wed Nov 25 2009 - 11:14:17 CST

I have noticed the discussion about ntt=3 parallel scaling so that I
used ntt=1 or ntt=2 and both did the same.

dawei

On Wed, Nov 25, 2009 at 12:10 PM, Carlos Simmerling
<carlos.simmerling_at_gmail.com> wrote:
> 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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