[gmx-users] Re: How does fourierspacing correspond to fourier_nx, fourier_ny, and fourier_nz?
Dommert Florian
dommert at icp.uni-stuttgart.de
Fri Apr 20 18:06:58 CEST 2012
On Fri, 2012-04-20 at 11:35 -0400, 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.
>
Yes, Gromacs uses the former specification and a setting of 0.12nm
Fourier spacing sounds much more reasonable.
/Flo
> Best wishes,
>
> Andrew DeYoung
> Carnegie Mellon University
>
--
Florian Dommert
Dipl. - Phys.
Institute for Computational Physics
University Stuttgart
Pfaffenwaldring 27
70569 Stuttgart
EMail: dommert at icp.uni-stuttgart.de
Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
Tel.: +49 - (0)711 - 68563613
Fax.: +49 - (0)711 - 68563658
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