[gmx-users] HREX simulation

Michael Shirts mrshirts at gmail.com
Fri Aug 28 17:23:15 CEST 2015

> The exchange attempt forces replicas to synchronize, and this forces the
> whole simulation system to pay the cost of any localized slow-down (e.g.
> network traffic congestion, internal simulation load imbalance from
> diffusion, even throttling of core clocks from heating effects) at each
> synchronization point. Longer periods between exchange attempts use
> resources more efficiently if the observed variations are approx random.

Excellent point.  I usually do low-core number replica exchange, but
when is running on lots of cores,  I can see how frequent exchange
would slow things down.

> That ought to be a problem, but in fact the replica-exchange implementation
> already synchronizes much more frequently than it should (
> https://gerrit.gromacs.org/#/c/4312/ needs more testing before this is
> solved).

Thanks for pointing that out, I had missed that proposed change.

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