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

From: James Starlight (jmsstarlight_at_gmail.com)
Date: Thu Jul 20 2017 - 06:03:29 CDT

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

There was no such error with this system running on CPU cluster. How I
should modify conf file to solve the issue?



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