From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Wed Nov 08 2006 - 10:40:51 CST
Are you not wrapping your coordinates? Is wrapAll on or off in the
config file? not present (it defaults to off)?
Anyway, the cell basis is the reality of the periodic system, not the
coordinates of the atoms (i.e. the box size). Sorry for the
confusion about that point.
On Nov 8, 2006, at 11:26 AM, Neelanjana Sengupta wrote:
> 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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