namd on AWS

From: Miro Astore (
Date: Tue Oct 01 2019 - 00:02:14 CDT

Hello everyone.

I am trying to run the namd AMI package and I'm not getting very good
performance. I've tried a few types of p2 and p3 node types and I can't get
comparable performance to my university's HPC clusters when running 2
workloads on the same node. ~200000 atom system. The performance doesn't
appear to be very different from copying over the precompiled binary from
the website. Just wondering if anyone else has encountered this issue.

Completely possible I'm just not running things in the correct way, so I
would be very interested to see how you guys run things.

Best, Miro

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