[gmx-users] Gromacs on CPU runs fine, same calculation crashes on GPU with nonbonded interaction larger than table limit

Justin Lemkul jalemkul at vt.edu
Wed Feb 28 19:15:07 CET 2018

On 2/28/18 1:13 PM, Marc Hoemberger wrote:
> Hi everyone,
> I ran a targeted md simulation with gromacs 5.1.4 + plumed 2.4.0 on a
> 32-core node. The simulation worked well, however when I wanted to try to
> run the identical simulation (same starting points etc) on a CPU/GPU node
> the run crashes with two warnings of the following type:
> WARNING: Listed nonbonded interaction between particles X and Y at distance
> Z which is larger than the table limit W nm.
> I know that my system is equilibrated well, and the same setup does work
> perfect on the CPU only run.
> For running the GPU run I use -ntomp 4 and one gpu, with -pin on. I use
> CUDA 7.0.28 and gromacs 5.1.4 with plumed 2.4.0.
> If there is any additional information that could help, let me know and I
> will provide it.

Can you reproduce the problem with a vanilla GROMACS version 
(non-PLUMED), preferably something newer?



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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