Re: Simulation of a membrane protein with large extracellular domains

From: Josh Vermaas (
Date: Thu Nov 13 2014 - 08:35:43 CST

Hi Fotis,

How large did you let "margin" get? I've had to use sizable margins
(~10) for initial runs with large transmembrane systems. For production,
I can get away with much smaller margins (1-3). If you've checked that
your initial x-y-z dimensions are reasonable, I believe there will be
some value for margin at which this error goes away.

-Josh Vermaas

On 11/13/2014 07:30 AM, Fotis Baltoumas wrote:
> Dear NAMD list,
> I have been trying to simulate (NPT and periodic boundary conditions) the
> theoretical model of a membrane protein containing not only the
> transmembrane segment (embedded in a POPC bilayer) but also its large
> extracellular domain, covered by solvent, with no success. The initial
> energy minimization part finishes successfully, however the simulation
> then immediately crashes, giving a fatal error about the size of the
> periodic cell:
> """
> 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.
> """
> Given that I have already successfully simulated the isolated
> transmembrane part of the protein using a "standard" (if there is such a
> thing) procedure for membrane simulations, I can only think that this
> crash occurs due to the large exomembrane domain of the model. I have
> tried increasing the margin and altering the values in the PBC options,
> with no success.
> The only thing I haven't tried yet is disabling useFlexibleCell which,
> however, is important for membrane simulations.
> Since in the model of the full protein the solvent& Extracelluler domain
> comprise most of the system, with the membrane/TM part being taking a
> smaller portion of the space, should I disable the flexible cell and
> simulate the system as I would do for a soluble protein? Or is there any
> other option available for this kind of problem?
> Thank you in advance,
> Fotis Baltoumas
> (P.S. I know I could just not use pressure control and be done with it,
> however I have already performed the transmembrane segment simulations
> using NPT conditions and I would like to maintain the protocol for the
> full body model as well.)

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