Re: periodic cell has become too small for original patch grid!

From: Eric H. Lee (ericlee_at_ks.uiuc.edu)
Date: Tue Nov 18 2008 - 03:22:03 CST

The PME grid size should be *larger* than your cell basis vectors, but
not too large as to compromise efficiency. Try 96-84-96 and see if
you get the same error.

-Eric

On Nov 18, 2008, at 2:54 AM, ydhuang2727 wrote:

> Hey, everyone!
>
> I come across an error like,
> periodic cell has become too small for original patch grid!
>
> Although, i have known that PMEGridSize should be chosen so that it
> can be factorized by 2, 3 or 5, still am i not determined on how to
> setup PMEGridSize according to cellBasisVector and i am, totally,
> not sure if my setup is right or wrong only based on sush a single
> rule.
> Firstly, please have a look at the following setup:
> # Periodic Boundary Conditions
> cellBasisVector1 93.0 0. 0.
> cellBasisVector2 0. 82.4 0.
> cellBasisVector3 0. 0. 90.5
> cellOrigin -8.449 54.259 48.939
> wrapAll on
>
> #I got the cellBasisVector poorly by hand, using Mouse/Label/Bond in
> VMD main menu. Is there any other good method for this?
>
> # PME (for full-system periodic electrostatics)
> PME yes
> PMEGridSizeX 96
> PMEGridSizeY 81
> PMEGridSizeZ 90
>
> Herein, my confusion is:
> can PMEGridSize be bigger or smaller than cellBasisVector?
> how do i get the right values?
>
> Thanks !!
> Good day!
>
> Dong,
>
>
> [广告] 金秋最关注楼盘-房不胜房

Eric H. Lee
Medical Scholars Program
Theoretical and Computational Biophysics Group, UIUC
ericlee_at_ks.uiuc.edu

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:50:06 CST