How to set values for cellBasisVector and PMEGridSize properly

From: ydhuang2727 (
Date: Mon Oct 20 2008 - 03:00:15 CDT


Hi everybody,
I am running a minimization and equilibration simulation on Glucokinase in a
water box. The simulation begins to run, but stops after a while because
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 don't understand why this is the case.I set cellBasisVector1,2,3 according to water box's size and PMEGridSizeX,Y,Z according to cellBasisVector.Since errors generated, i desperately want to know how to set these values properly for a specified system. following is part of my configure file.

Assume the length of my water box is 72.15(X-dimension), width is 91.29(Y-dimension) , height is 75.28(Z-dimension).

# Periodic Boundary Conditions
cellBasisVector1 72.15 0. 0.
cellBasisVector2 0. 91.29 0.
cellBasisVector3 0. 0. 75.28
cellOrigin 30.6 0.4 70.4

# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 75

PMEGridSizeY 96

PMEGridSizeZ 80


Thank you for your attention,
Yandong Huang


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