From: Ashkan Shekaari (shekaari_at_email.kntu.ac.ir)
Date: Sun Apr 19 2020 - 18:10:32 CDT
Margins and timestep are very important parameters to keep from such an error.
Use: margin 3.0
-- All the best, Ashkan Shekaari, Ph.D Candidate in Solid State Physics, K. N. Toosi University of Technology, Tehran, Iran From: "Khoualdi Asma Feriel" <asma.feriel.khoualdi_at_umontreal.ca> To: "namd-l" <namd-l_at_ks.uiuc.edu> 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. Sincerely, Asma Feriel
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