On 21/04/2012 1:35 AM, Andrew DeYoung wrote:
Hi Florian and Mark,
Thank you for your time!
I am actually using (fourier_nx, fourier_ny, fourier_nz) ~ (14, 14, 125).
This is what a colleague who has recommended, although she is using a
different (somewhat slower) MD package. One question, if you have time. In
that other code, one specifies the maximum number of wave vectors along each
(positive or negative) direction. So specifying (14, 14, 125) in that codes
means "use 14 vectors along +x, use 14 vectors along -x; use 14 vectors
along +y, use 14 vectors along -y; use 125 vectors along +z, use 125 vectors
along -z". So that corresponds to something like (28, 28, 250) or (29, 29,
251) actual grid points, I think. But in the Gromacs manual
(http://manual.gromacs.org/current/online/mdp_opt.html#ewald), I am not sure
if fourier_nx, fourier_ny, and fourier_nz specify "the number of grid points
along x, y, and z" or "the number of vectors to use along +x and -x; +y and
-y; and +z and -z". I think that Gromacs uses the former, but I am not
sure.
The former for PME. The latter for plain Ewald (which you should
probably not want to use).
Mark
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