Recently, a few algorithms have been developed to enable massively parallel
computation which can efficiently use hundreds of CPUs simultaneously for MD
simulation. For example, J Comput Chem 26: 1318–1328, 2005.
Is there a plan to implement such algorithm in Amber/PMEMD? As computer
cluster is getting cheaper and cheaper, the cluster size keeps expanding
quickly as well. Such algorithms should be very helpful and indispensable to
reach >ms scale simulation.
Thanks,
Mingfeng
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Received on Wed May 21 2008 - 06:07:39 PDT
