Re: [AMBER-Developers] ncsu hooks

From: Volodymyr Babin <>
Date: Fri, 22 Oct 2010 11:03:10 -0400 (EDT)


> 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.

> 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.

> 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.

With kind regards,


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Received on Fri Oct 22 2010 - 08:30:03 PDT
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