Re: CUDA-accelerated NAMD does not support NBFIX parameters [RESOLVED]

From: Axel Kohlmeyer (
Date: Mon Sep 14 2009 - 15:57:12 CDT


On Mon, Sep 14, 2009 at 8:24 AM, Héctor Urbina <> wrote:
> OK, I changed the system to another without NBFIX parameters. Now I'm
> getting huge energetic values, after 100 steps of minimization, the
> output just says nan :(, but the NBFIX error message is not being
> showed. The minimization of the same system using normal namd run
> just fine.

please keep in mind, that namd-gpu uses single precision for the
non-bonded force calculations, so you are more vulnerable to overflow
errors, when your structure has high potential energy. people that have
used or are using the single precision version of gromacs are very familiar
with this and often it is required to "pre-minimize" with the double
precision version before you can use the single precision version without
the run crashing upon you.


> Thanks Axel,
> cheers.
> --
> Hector Urbina S.

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.

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