Re: namd-l digest V1 #2927

From: Raman Preet Singh (
Date: Mon Aug 24 2020 - 01:45:58 CDT


I recently encountered the same issue with all-atom simulations and shared my tweaks at the link below.


Not sure if this works with you but can be a point to look at.


From: namd-l digest <>
Sent: Monday, August 24, 2020, 11:40 AM
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


Date: Sun, 23 Aug 2020 11:44:55 -0400
From: Victor Kwan <>
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 <> 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


End of namd-l digest V1 #2927

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