String Method with Swarms of Trajectories (SMwST) Performance

From: Alexander Adams (
Date: Thu Jul 11 2019 - 10:43:25 CDT

Dear NAMD users,

I am attempting to perform SMwST on a membrane embedded transport protein,
as done in the Exploring Complex Transition Pathways tutorial
achieve expected performance (several hours/iteration) for ~20 iterations,
then experience a dramatic slowdown where it is common for runs of a single
iteration to time out after 24-48 hours. I've experienced this on 2
separate clusters and see only minor (<10%) changes in NAMD's reported
performance speed. I have noticed that most of the failed runs have the
memory usage swell from 700 Mb to 93 Gb, though some still complete despite
this behavior.

I apologize for the slim information, but I'm not sure what will best help
in the debugging process. Thanks in advance for your assistance!

Alex Adams

University of Michigan, Ann Arbor
Ph.D. Candidate - Mayes Lab
College of Engineering - Chemical Engineering

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2019 - 23:20:52 CST