Re: Atoms moving too fast only with CUDA version.

From: Aron Broom (
Date: Wed Jun 27 2012 - 00:51:33 CDT

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

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


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.
> Regards.
> Amin.
> ______________________________________________________________________
> सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
> Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
> सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
> पिन कोड/PIN CODE :160036
> दूरभाष/EPABX :0172 6665 201-202

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:21:43 CST