it usually takes programs some time before they become efficient. the
spatial decompositino and load balancing are not ideal at the start.
additionally, much work needs to be done to start running MD, such as
reading and writing to disk, setting up the arrays, and so on.
stopping the program each ps or less would be quite slow. are you in a
situation where you have no way to access more than 1 CPU?
On Tue, Aug 23, 2011 at 3:39 PM, Dmitry Mukha <dvmukha.gmail.com> wrote:
> I mean after exchange all replicas should pass equal time path. If you store
> results for each replica making it waiting for others, you can accomplish
> the exchange after the moment last replica achieved N steps. Then we can
> repeat iteration.
>
> 2011/8/23 Adrian Roitberg <roitberg.qtp.ufl.edu>
>
>> Hi
>> I am not sure at all what you mean by "serial (step-by-step)"
>>
>> In any case, unless something strange happens, pmemd will be released in
>> amber12 (april 2012??) with native remd capabilities. The GPU version
>> might also be released then if we can get it working efficiently.
>>
>>
>> On 8/23/11 3:24 PM, Dmitry Mukha wrote:
>> > serial (step-by-step)
>>
>> --
>> Dr. Adrian E. Roitberg
>> Professor
>> Quantum Theory Project, Department of Chemistry
>> University of Florida
>> roitberg.ufl.edu
>>
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>>
>
>
>
> --
> Sincerely,
> Dmitry Mukha
> Institute of Bioorganic Chemistry, NAS, Minsk, Belarus
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Received on Tue Aug 23 2011 - 13:00:06 PDT
