[gmx-users] replica exchange

Mark Abraham Mark.Abraham at anu.edu.au
Thu Jan 12 16:44:30 CET 2006

Marc F. Lensink wrote:
> dear,
> 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 don't believe you are really observing gromacs REMD running on a 
low-latency network and not on a higher latency network. If you can 
install LAM MPI on a system, parallel gromacs (and thus gromacs REMD) 
will run on it. Probably you are observing a problem with your MPI 
installation, or gromacs doesn't like your MPI installation.

> 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!

Of course!

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

MPICH is not supported/recommended. LAM is. Please read the 
documentation on the gromacs webpage.


More information about the gromacs.org_gmx-users mailing list