[gmx-users] replica exchange

Marc F. Lensink lensink at scmbb.ulb.ac.be
Thu Jan 12 15:52:52 CET 2006


congratulations to the gmx developers for their implementation of the
replica exchange algorithm.

however, i noticed that the use of remd requires low-latency network
communication, because when using simple ethernet no communication can
be established.

i do not understand why this is.  replica's only need to talk to their
neighbours, and only then every so many simulation steps.  for that,
communication by phone should be enough!

i'm talking about 16-20 replica's ie cpu's (8-10 nodes).  using mpich,
not lam.


Marc F. Lensink           http://www.biochem.oulu.fi/~lensink/
Centre for Structural Biology and Bioinformatics         SCMBB
Université Libre de Bruxelles          lensink at scmbb.ulb.ac.be
Boulevard du Triomphe - CP 263, B-1050 Brussels, Belgium
tel: +32 2 650 5411  secr: +32 2 650 2013  fax: +32 2 650 5425

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