Re: Patch grid too small error in first production run

From: Josh Vermaas (
Date: Sun Apr 19 2020 - 16:51:22 CDT

Hi Asma,

What is your margin set to in the first production step? For membrane
simulations I've sometimes needed to set it to 5 or 7 if there is a
lipid hanging over the edge of the box by a bunch. The other thing to
check would be how the box sizes are set. I'm not super familiar with
how CHARMM-GUI does it, but if your box changed alot during
equilibration, it wouldn't surprise me if CHARMM-GUI set this incorrectly.


On 4/19/20 1:29 PM, Khoualdi Asma Feriel wrote:
> Dear all,
> I have seen many solutions proposed for this error on mailing list - I
> used restart files for circumventing this problem earlier to continue
> equilibration steps and this worked. But the problem now is that I am
> trying to run the first "production" run (step7_production.inp) and
> when I use the restart files from last step 6.6_equilibration.inp, I
> still get only the step7 xst file with 0 steps and error persists. 
> Please guide me to how to solve this problem , knowing that I am
> running using NPT and don't want to change to NVT. I a still learning
> NAMD and have seen that margin increase should not affect my
> simulation, just the "performance", but I am not sure to which value
> it should be set/ how to determine best value that doesn't;t impede or
> affect my simulation.
> Sincerely,
> Asma Feriel

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