there would almost certainly be no advantage, and probably much worse,
compared to running REMD with sander. can you tell us what about
sander REMD isn't working for you? or are you looking for some way to
run REMD in serial, no matter what program?
Regarding stretching of intervals, you should check work on that by
the Roitberg lab.
"Exchange frequency in replica exchange molecular dynamics." Daniel
Sindhikara, Yilin Meng, Adrian E. Roitberg. J. Chem. Phys. 128, 024103
(2008)
as well as some more recent work
On Tue, Aug 23, 2011 at 3:35 PM, Dmitry Mukha <dvmukha.gmail.com> wrote:
> Yes, restarting might be inefficient, but with lack of cluster resources
> REMD cannot be performed at all in a reasonable time with proper density of
> replicas over temperature parameter. And intervals may be stretched.
>
> 2011/8/23 Carlos Simmerling <carlos.simmerling.gmail.com>
>
>> 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
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>> _______________________________________________
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>
>
>
> --
> Sincerely,
> Dmitry Mukha
> Institute of Bioorganic Chemistry, NAS, Minsk, Belarus
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Aug 23 2011 - 13:00:04 PDT
