Re: Patch grid too small error in first production run

From: Josh Vermaas (joshua.vermaas_at_gmail.com)
Date: Sun Apr 19 2020 - 20:19:53 CDT

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> 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> on behalf of Josh Vermaas <
> joshua.vermaas_at_gmail.com>
> *Sent:* April 19, 2020 5:51 PM
> *To:* namd-l_at_ks.uiuc.edu <namd-l_at_ks.uiuc.edu>; Khoualdi Asma Feriel <
> 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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