[gmx-users] Replica exchange questions
David van der Spoel
spoel at xray.bmc.uu.se
Tue Oct 11 15:54:00 CEST 2005
On Tue, 2005-10-11 at 15:10 +0200, Marc Baaden wrote:
> 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 some
> 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
More information about the gromacs.org_gmx-users