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Truncated octahedral in NAMD

posted Oct 8, 2011, 9:04 AM by Dong Xu

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).

see http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/9949.html
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