NAMD 2.12 released

From: Angelo Rossi (
Date: Mon Dec 26 2016 - 15:53:42 CST

Dear Jim:

Excellent! As they say in New York, I like it already.

By that, I mean the QM/MM new feature. The example that was included
worked "right out of the box" utilizing the NAMD/ORCA interface. This
really opens many new opportunities.

I do have one comment, however. ORCA, as it is distributed to the general
public, runs on a single SMP node. For example, I ran NAMD 2.12
(Linux-x86_64-muticore)/ORCA, and it worked fine.

But, what happens when one runs NAMD (Linux-x86_64-ibverbs)/ORCA? The QM
component would have to run on only one of the nodes in the selection.
Doesn't this eventually present a bottleneck situation where the MM
component waits for the QM to finish? I understand that is the case
always, but as more nodes are added, this becomes the dominant delay.
Other QM/MM codes may not have this problem (e.g. NWChem), since both QM
and MM components are parallelized (though the MM component not as well as


Warm regards,


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