From: Raman Preet Singh (ramanpreetsingh_at_hotmail.com)
Date: Mon Aug 24 2020 - 01:45:58 CDT
Ethan:
I recently encountered the same issue with all-atom simulations and shared my tweaks at the link below.
h<http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2019-2020/1531.html>ttp://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2019-2020/1531.html<http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2019-2020/1531.html>
Not sure if this works with you but can be a point to look at.
Best
RPS
________________________________
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Sent: Monday, August 24, 2020, 11:40 AM
To: namd-l-digest_at_ks.uiuc.edu
Subject: namd-l digest V1 #2927
namd-l digest Monday, August 24 2020 Volume 01 : Number 2927
In this issue:
Re: namd-l: Simulation Crash SMD Coarse-Grained
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Date: Sun, 23 Aug 2020 11:44:55 -0400
From: Victor Kwan <vkwan8_at_uwo.ca>
Subject: Re: namd-l: Simulation Crash SMD Coarse-Grained
Why don't you just restart from a recent checkpoint? This question has been
discussed extensively on the mailing list.
On Wed, Aug 19, 2020 at 4:24 PM Ethan Croitoru <ecroitoru1_at_gmail.com> wrote:
> Hi,
>
> I am running steered MD on a coarse-grained transmembrane helix with cg
> membrane, water, and ions, using martini. I am running this using the
> distance colvar, just to see what that will look like and see how to better
> define the pathway. The simulation crashed saying:
>
> FATAL ERROR: Periodic cell has become too small for original patch grid!
> Possible solutions are to restart from a recent checkpoint,
> increase margin, or disable useFlexibleCell for liquid simulation.
>
> I have experienced this error before running npt on the coarse grain
> system and just decreased the timestep to fix that, but now my timestep is
> already on the lower side for coarse-grained systems and, and I am
> currently increasing margin, but I was wondering if anyone had other ideas
> on preventing this issue.
>
> Best,
> Ethan
>
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