Re: PME GridSize

From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Wed Nov 08 2006 - 10:26:15 CST

Just a re-confirmation: The PMEGridSize(X, Y, Z) should be greater than or
equal to the Box Size, and NOT greater than or equal to the Cell Basis?

Upon loading a previous trajectory, "molinfo top get a", etc, give me ~ 55.0
.

However, when I do a selection "set all [atomselect top all]",
"measure minmax $all" gives,
{-127.4 -109.5 -142.2} {107.6 155.9 137.6}
corresponding to lengths 235, 266, 280 (approx) along X, Y, Z.

So should my PMEGridSizes be ~ 60, or ~ 280 ?

Your remarks are highly appreciated.
Thanks,
Neelanjana

On 11/7/06, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
>
> You are right, they should be around the size of your box (or a little
> bigger). They should also ideally be multiples of 2, 3, and 5.
> If they are too low, you will have a grid of charges that very poorly
> mimics the actual distribution. I'm not sure how it will affect the
> simulation but results will be inaccurate.
>
>
> On Nov 7, 2006, at 6:57 PM, Neelanjana Sengupta wrote:
>
> Hello,
>
> As per my thinking, the PMEGridSizeX, PMEGridSizeY and PMEGridSizeZ should
> be greater than (or at least equal to), the lengths along the X, Y and Z
> axes of the simulation box (assuming cubical box).
> Could somebody point out if my thinking is not correct, and how the
> PMEGridSizes affects the accuracy of the simulation results?
>
> Thanks and regards,
> --
> ****************************************
> Neelanjana Sengupta, PhD student
> Dept. of Chemistry
> Univ. of California-Irvine
> Irvine, CA 92697
> USA
> Phone: 1-949-824 9921
> email: sengupta_at_uci.edu
> ****************************************
>
>
>

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