Re: How to set values for cellBasisVector and PMEGridSize properly

From: Anirban Ghosh (anirbang_at_cdac.in)
Date: Mon Oct 20 2008 - 08:30:23 CDT

Hi,

You can find the correct size of the water box for your protein by using
the "measure minmax" command in VMD's TK Console. You should also disable
the useFlexibleCell option. Try to run your simulation under constant
volume condition without using constant pressure. Hope this will solve
your problem.

Regards,

>
>
>
>
> 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
> 117
>
>
>
> Thank you for your attention,
> Yandong Huang
>
>

-- 
Anirban Ghosh
Grade Based Engineer
Bioinformatics Team
Scientific & Engineering Computing Group
Centre for Development of Advanced Computing
Pune, India

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:48:30 CST