Re: "Periodic cell has become too small for original patch grid!" with membrane system on GPU

From: David Hardy (
Date: Fri Aug 25 2017 - 14:39:24 CDT

Dear Gleb,

I've found and fixed a long-standing bug in the NAMD 2.12 CUDA kernels that may have affected your simulation. You might want to try the NAMD nightly build from <> to see if you are able to run on your GPU.

Best regards,

David J. Hardy, Ph.D.
Theoretical and Computational Biophysics
Beckman Institute, University of Illinois
> On Jul 20, 2017, at 6:03 AM, James Starlight <> wrote:
> Dear NAMD Users!
> I have faced with a following problem running the lattest NAMD with
> GPU quadro 5000k. I am dealing with the GPCR-membrane system
> assembling with the CHARM-GUI with all input conf files provided on
> the default.
> I took the system just after the equilibration and running it with the
> CHARM-GUI parameters obtained the following error:
> FATAL ERROR: Periodic cell has become too small for original patch grid!
> Possible solutions are to restart from a recent checkpoint,
> increase margin, or disable useFlexibleCell for liquid simulation.
> because this is a membrane-consisting system and disable
> useFlexibleCell is not possible I try  to increase margin up to 5.0,
> obtaining another error:
> FATAL ERROR: High global CUDA exclusion count!  (96033 vs 92328)
> System unstable or pairlistdist or cutoff too close to periodic cell
> size.
> There was no such error with this system running on CPU cluster. How I
> should modify conf file to solve the issue?
> Thanks!
> Gleb

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