[gmx-users] Replica exchange questions

Moore, Jonathan (J) JMoore2 at dow.com
Tue Oct 11 16:01:27 CEST 2005

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-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of David van der Spoel
Sent: Tuesday, October 11, 2005 9:54 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Replica exchange questions
Importance: Low

On Tue, 2005-10-11 at 15:10 +0200, Marc Baaden wrote:
> Hi,
> we are planning to use replica exchange very soon on a rather big 
> system. What is the current state in Gromacs ? Eg:
> * which Gromacs version is recommended for replica exchange, 3.3 or CVS or
>   custom version ?

> * are there known bugs/shortcomings ?

> * can the individual replicas be parallelized ? Eg could one run 20
replicas, each
>   using 16 procs or can a replica only run on a single CPU ?
No. We'll work out how to do it and then put it in a subsequent version. If
it is relatively easy we might backport it to 3.3.x (but not 3.3.0).

> * are there any RE tutorials for gromacs ?
We have a paper in proof at JMB (Seibert et al. can be downloaded if you
have a subscription) which has some equations.

> Thanks in advance,
>   Marc Baaden
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of
Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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