what do you mean by step by step? running a few hundred steps of MD
then stopping and running a different replica? based on how pmemd
works, this would be very inefficient.
There are indeed plans for the future versions of amber to have native
REMD inside pmemd.
On Tue, Aug 23, 2011 at 3:24 PM, Dmitry Mukha <dvmukha.gmail.com> wrote:
> Is there among Amber developers the idea to implement serial (step-by-step)
> REMD using pmemd.cuda?
>
> ---------- Forwarded message ----------
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> Date: 2011/8/23
> Subject: Re: [AMBER] Is it possible to do REMD for a 12000 atom molecule?
> To: AMBER Mailing List <amber.ambermd.org>
> your question isn't clear. REMD should not be much slower than
> standard MD for the same system in sander. Did you compare these?
>
>>
>
> --
> Sincerely,
> Dmitry Mukha
> Institute of Bioorganic Chemistry, NAS, Minsk, Belarus
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>
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Received on Tue Aug 23 2011 - 12:30:05 PDT
