Re: MD simulation Patch grid errors

From: Thomas Evangelidis (
Date: Tue Jan 07 2014 - 17:56:32 CST

Do you see anything strange happening to the unit cell? What lipid force
field do you use? If you use AMBER lipid11 then surface tension is required
but for CHARMM I guess not. Have you looked into the protein-membrane NAMD

You error occurs because the unit cell is adapting to the imposed pressure
and one or more of the cellBasisVectors have become larger than the
respective PMEGridSizes. Just adjust the PMEGridSize vectors and continue
the simulation from where it stopped. Alternatively, you can let NAMD
choose the optimum PME grid dimensions by replacing the relevant section of
your configuration file with the following:

#PME (for full-system periodic electrostatics)
PME yes
PMEGridSpacing 1 ;# set this to 1 to allow NAMD to choose the PME
grid dimensions
# Comment out PMEGridSize[XYZ] to allow NAMD to adapt them automatically to
effective values.
#PMEGridSizeX 108
#PMEGridSizeY 108
#PMEGridSizeZ 84

Note that you will probably need to continue the simulations many times
until the system equilibrates and the box dimensions stop to change. When
the box size is stabilized you can comment out PMEGridSpacing and assign
values to PMEGridSizeX, PMEGridSizeY and PMEGridSizeZ.

On 8 January 2014 01:33, Jiann George Pazhamalil

> Dear NAMD users,
> I am a student and extremely new at this process and I am trying to run a
> protein and membrane simulation where I am receiving the error "FATAL
> ERROR: Periodic cell has become too small for original patch grid!" I am
> aware that this is a common problem and I have been looking at the archives
> however increasing the margin or restarting the run is not helpful and I am
> still receiving this error and with a membrane, I can't switch off
> flexiblecell. Energy minimization and equilibration is running fine but the
> problem is with the MD run which is unique from the previous problems seen
> on the list. I am a little unsure about the surfaceTensionTarget value I am
> using. I have a POPC bilayer and I'm using 17 dyn/cm, could that possibly
> be the reason of the error?
> Regards,
> Jiann

Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
157 71 Athens


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