Simulation Crash SMD Coarse-Grained

From: Ethan Croitoru (
Date: Wed Aug 19 2020 - 15:24:01 CDT


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.


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