Re: NAMD 2.6 - PME Error on Large Protein-DNA System!

From: Peter Freddolino (
Date: Wed Feb 27 2008 - 23:59:41 CST

Hi Sean,

> I did some digging and tried the following (while supplying the SAME
> random seed to keep things consistent):
Please note that if you're doing langevin dynamics in parallel, this
still doesn't guarantee identical results because of non-determinism in
communication ordering and the way the NAMD rng works. There have been a
few threads in the past 6 months on namd-l on this subject, if you're
> I would really appreciate if anybody could help explain this behaviour
> and welcome any comments, questions, or feedback that would help solve
> this problem!
Given the troubleshooting you've already tried (and thank you for noting
what you've done!), the next likely culprit is changes in your periodic
cell size that are too large. I'd recommend checking two things:
-see how much your periodic cell size changes over the course of the run
-if you restart your simulation from the restart files saved before the
crash, does it run fine or crash again?

This should (hopefully) help to find whatever is going on here.


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