Re: Patch grid too small error in first production run

From: Ashkan Shekaari (
Date: Sun Apr 19 2020 - 18:10:32 CDT

Dear Khoualdi,

Margins and timestep are very important parameters to keep from such an error.
Use: margin 3.0
timestep 1.0

All the best, 
Ashkan Shekaari, 
Ph.D Candidate in Solid State Physics, 
K. N. Toosi University of Technology, 
Tehran, Iran 
From: "Khoualdi Asma Feriel" <> 
To: "namd-l" <> 
Sent: Sunday, April 19, 2020 11:59:06 PM 
Subject: namd-l: Patch grid too small error in first production run 
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. 
Asma Feriel 

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