Re: Simulation Crash SMD Coarse-Grained

From: Victor Kwan (
Date: Sun Aug 23 2020 - 10:44:55 CDT

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

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