Simulation of a membrane protein with large extracellular domains

From: Fotis Baltoumas (
Date: Thu Nov 13 2014 - 07:30:54 CST

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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