Hi
>> I'm modifying amber 11 to change the way replica exchanges are done.
>> Specifically, sometimes replicas don't have an exchange partner, so they
>> just keep on simulating at the same temperature.
>>
>
> More details would help me to understand the problem better.
>
>
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. But
it should still do it's "updates" like you mention below, no?
>> Now I don't really get what these ncsu hooks are and do, nor do I really
>> know what NCSU stands for.
>>
>
> You are right, this stuff is there to confuse you.
>
>
hmm....
>> But most importantly, could you tell me if
>> it's necessary that each replica calls on_delta and on_exchange at each
>> turn?
>>
>
> "necessary" for what?
>
> "on_SOMETHING" are simply callbacks that are called when certain
> events happen in sander main loop; such as "delta E is being evaluated
> for an exchange attempt" and "exchange is in progress"; NCSU codes
> (this is just a namespace -- pseudo-random combination of letters)
> then take appropriate actions (like compute some contributions to
> the delta E or change context after an exchange).
>
>
>> If so what should I do? call it with itself as argument? because
>> these functions are taking another replica number as argument. I'd
>> really appreciate your help.
>>
>
> The easiest way would be to just ignore all these on_* things.
>
>
ok...
thanks for the help!
Yannick
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Received on Fri Oct 22 2010 - 09:00:07 PDT
