great, thanks for your help!
Yannick
Volodymyr Babin wrote:
> Hi,
>
>
>> I'm implementing replica exchange with random neighbor pairs. That is
>> you don't have the restriction to exchange with the left on even time
>> steps and the right on the odd, also allowing for an odd number of
>> replicas. I just generate a list of pairs and try to exchange each time.
>> Regarding my problem, sometimes a replica ends up with no partner.
>>
>
> Please take a look at ncsu-bbmd-hooks.f: it implements REMD between
> random pairs of replicas (including even number of replicas); the
> list of exchange partners is constructed by random shuffling of the
> (1 ... Nr) array and then trying to exchange consecutive pairs.
> The code is tailored towards NCSU stuff, but you can probably reuse
> some ideas. Please see example runs at
>
> http://ambermd.org/tutorials/advanced/tutorial11/index.html
> http://ambermd.org/tutorials/advanced/tutorial12/index.html
>
> The code is not restricted to "biased" things and can be used
> easily for temperature exchange REMD as well (input looks somewhat
> unexpected in that case though).
>
>
>> But
>> it should still do it's "updates" like you mention below, no?
>>
>
> (a) If a replica is not planned to participate in exchange, there
> is no need to do anything exchange-related. (b) Calls to
> on_delta/on_exchange will attempt to mpi_sendrecv() for a given pair
> (if needed, i.e., if some of the ncsu stuff is active).
>
>
>> ok...
>>
>
> If none of ncsu_* things is present in the MDINs, there is no need
> to call any of the on_* callbacks (except init/fini/on_mdread, so that
> the ncsu-* things know they are not active). You can probably proceed
> ignoring them all; I can later adjust things as needed for ncsu stuff
> to work properly.
>
> Have a nice day,
>
> Volodymyr
>
>
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Received on Fri Oct 22 2010 - 09:30:04 PDT
