Re: truncated octahedral

From: Nicholas M Glykos (glykos_at_mbg.duth.gr)
Date: Tue May 05 2009 - 05:18:15 CDT

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/

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