From: Khoualdi Asma Feriel (asma.feriel.khoualdi_at_umontreal.ca)
Date: Thu Apr 30 2020 - 12:16:01 CDT
Thank you all very much
Asma Feriel
Get Outlook for iOS<https://aka.ms/o0ukef>
________________________________
From: Josh Vermaas <joshua.vermaas_at_gmail.com>
Sent: Sunday, April 19, 2020 9:19:53 PM
To: Khoualdi Asma Feriel <asma.feriel.khoualdi_at_umontreal.ca>; NAMD list <namd-l_at_ks.uiuc.edu>
Subject: Re: namd-l: Patch grid too small error in first production run
Yeah. The default margin (1 I think) is often too small. Try 3 or 5. That has worked for me in the past.
Josh
On Sun, Apr 19, 2020, 5:06 PM Khoualdi Asma Feriel <asma.feriel.khoualdi_at_umontreal.ca<mailto:asma.feriel.khoualdi_at_umontreal.ca>> wrote:
Hi,
Thanks for your time and reply. So for the margin, there is no margin set in the default production configuration file. I assume that this means it is the default.
I visualized the lipid membrane and protein structure box that charmmGUI generated before equilibration started and the lipid wasn't hanging over the edge. I don't know if there is a way to visualize if this changes over the equilibration steps, yet.
As for the size,I don't know how big should a change be to be significant but here is the size at different steps.
I assume the solution is to set the margin to 5 and that shouldn't affect my simulation and normally would circumvent the problem.
--step 6.1 ----
# NAMD extended system configuration output file
#$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z
60000 127.961206 0 0 0 127.961206 0 0 0 120.405 0 0 0
----6.2-----
# NAMD extended system configuration output file
#$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z
100000 127.961206 0 0 0 127.961206 0 0 0 120.405 0 0 0
---6.3------
# NAMD extended system configuration output file
#$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z s_x s_y s_z s_u s_v s_w
158500 130.695039683 0 0 0 130.695039683 0 0 0 105.157080378 0 0 0 3.81017527134e-05 3.81017527134e-05 -2.63487416057e-05 0 0 0
---6.4--------
# NAMD extended system configuration output file
#$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z s_x s_y s_z s_u s_v s_w
200000 131.545258282 0 0 0 131.545258282 0 0 0 104.026770726 0 0 0 9.44947748104e-05 9.44947748104e-05 -0.000111273559608 0 0 0
---6.5----
# NAMD extended system configuration output file
#$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z s_x s_y s_z s_u s_v s_w
250000 131.543755032 0 0 0 131.543755032 0 0 0 104.40068353 0 0 0 3.24061549183e-05 3.24061549183e-05 9.80684731569e-05 0 0 0
---6.6-----
# NAMD extended system configuration output file
#$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z s_x s_y s_z s_u s_v s_w
300000 131.991955217 0 0 0 131.991955217 0 0 0 103.637757158 0 0 0 -5.14722488987e-05 -5.14722488987e-05 -2.58852612303e-05 0 0 0
________________________________
From: Josh Vermaas <yoshi121212_at_gmail.com<mailto:yoshi121212_at_gmail.com>> on behalf of Josh Vermaas <joshua.vermaas_at_gmail.com<mailto:joshua.vermaas_at_gmail.com>>
Sent: April 19, 2020 5:51 PM
To: namd-l_at_ks.uiuc.edu<mailto:namd-l_at_ks.uiuc.edu> <namd-l_at_ks.uiuc.edu<mailto:namd-l_at_ks.uiuc.edu>>; Khoualdi Asma Feriel <asma.feriel.khoualdi_at_umontreal.ca<mailto:asma.feriel.khoualdi_at_umontreal.ca>>
Subject: Re: namd-l: Patch grid too small error in first production run
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.
-Josh
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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