[gmx-users] replica exchange
David van der Spoel
spoel at xray.bmc.uu.se
Fri Jan 13 11:13:54 CET 2006
> On Thu, 12 Jan 2006 21:41:28 +0100
> David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>> Andrea C. Vaiana wrote:
>>> We're using mpich-1.2.4 and it does'nt hang with anything from 2 to
>>> 48 replicas. What I do see is a ~20% difference in performance
>>> between the 2 and 48 replicas, can anyone explain this? Would it
>>> just be sufficient to switch to LAM to get optimal performance?
>> this is due to the different density, you will see that at high
>> temperature fewer inteeractions are calculated.
> should this increase the speed ??
Yes, as long as the PME grid is the same.
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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