AW: Atoms moving too fast only with CUDA version.

From: Norman Geist (
Date: Wed Jun 27 2012 - 01:43:14 CDT



I had the same problem when I had a broken GPU. If you have multiple GPUs, try them separately to see if it only crashes when a special GPU participates.

Also it would be important if you get the error directly at start or later.


Good luck


Norman Geist.


Von: [] Im Auftrag von Aron Broom
Gesendet: Mittwoch, 27. Juni 2012 07:52
Betreff: Re: namd-l: Atoms moving too fast only with CUDA version.


I'm not sure you necessarily did anything wrong. I would suggest that your system even after 50,000 steps still has some kind of problems, but the CPU integrator is robust enough to muscle through it, whereas the CUDA one is not.

You should consider slowly heating your system from say 100K or something of the sort, as I would imagine you have jumped straight to 300K which generally works, but requires a decent starting point.

Keep in mind that even though the minimizer in NAMD is smarter than just steepest descent, it will still be easily trapped in local minima, so doing more minimization without some kind of dynamics is unlikely to get you closer to the global minimum and away from whatever problems you have.

Did you have a look at the structure also, and which atoms are causing the problem?


On Wed, Jun 27, 2012 at 1:37 AM, <> wrote:

Dear all,
    I am trying to run an equilibration using NAMD 2.9-CUDA on Linux. However,
I keep getting "Atoms moving too fast error".I increased the minimization
upto 50000 steps but it doesn't work. But when I tried to run the exact
same config file using the non-CUDA version it ran without any error even
at 10000 minimization steps.And the error is reproducible. Can someone
please tell me what may have gone wrong.



सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
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Aron Broom M.Sc
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Department of Chemistry
University of Waterloo

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