Re: How to set values for cellBasisVector and PMEGridSize properly

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Oct 20 2008 - 07:06:16 CDT

This is a fairly common problem that occurs when you start with a
periodic cell size that is much larger than the equilibrium volume of
your system in an NPT simulation (or, viewed another way, it reflects
insufficient initial solvation for the chosen box size). Have you tried
following the solutions proposed in the error message? You can also try
starting with a smaller periodic cell, or inspect your trajectories to
see if the system is shrinking due to lack of water.
Best,
Peter

ydhuang2727 wrote:
>
> 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
> 9129(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
> 117
>
> Thank you for your attention,
> Yandong Huang
>
>
>
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