Re: truncated octahedral

From: daniel aguayo (bioquimico_at_gmail.com)
Date: Tue May 05 2009 - 10:16:12 CDT

Tks Nicholas. That's the answer that I looking for.

On Tue, May 5, 2009 at 6:18 AM, Nicholas M Glykos <glykos_at_mbg.duth.gr>wrote:

>
> Hi Daniel,
>
>
> > How are the grid points distributed along the space?
>
> The grid for the FFT is calculated in the crystallographic (so to speak)
> frame, not along the orthogonal axes. In the case of a truncated
> octahedral cell -and depending on how you prepared your system- your cell
> basis vectors will possibly look similar to this :
>
> d 0 0
> 0 d 0
> d/2 d/2 d/2
>
> and your NAMD script file may contain something similar to this:
>
> cellBasisVector1 32.00 0.00 0.00
> cellBasisVector2 0.00 32.00 0.00
> cellBasisVector3 16.00 16.00 16.00
> cellOrigin 0.00 0.00 0.00
>
>
> The length of the third axis is sqrt( 3 * 16^2 ) = 27.7, so a possibly
> suitable PME grid for this case would be 32 x 32 x 27 (with 27 being 3^3,
> a good number for FFTW).
>
> Nicholas
>
> --
>
>
> Dr Nicholas M. Glykos, Department of Molecular Biology
> and Genetics, Democritus University of Thrace, University Campus,
> Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
> Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/>
>
>

-- 
saludos desde el fin del mundo

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