[gmx-users] Ewald sums too slow?
lindahl at csb.stanford.edu
Tue Jun 15 22:10:33 CEST 2004
My guess would be you are using the default nx=ny=nz=32.
If you look at the mdp documentation it says that these numbers specify
the number of reciprocal wave vectors in each dimension when you do
classical Ewald, while it is the number of grid cells with PME.
Fourierspacing doesn't enter for classical Ewald since you don't have a
If memory serves me right (but please check the literature on this),
reasonable "normal" numbers are in the order of 5, and in any case I'm
pretty sure 32 is massive overkill.
We've also optimized our PME implementation quite a bit compared to Tom
Darden's original implementation (a factor 2-3), so I would expect the
crossover system size to be very small.
The only reason why we have classical Ewald is to check the PME
On Jun 15, 2004, at 7:47 PM, Vincent Ballenegger wrote:
> Hi all,
> For small systems (<100 molecules), I would expect the standard Ewald
> sum to be faster than the PME method.
> For a system of 64 SPC water molecules in a box of width L=1.2413 nm,
> I found however that gromacs-3.2.1 is about 85 times slower when using
> the standard Ewald method instead of PME !!
> Why are the Ewald sums so slow?
> My input parameters were:
> ewald_rtol = 1e-05
> fourierspacing = 0.12
> rlist = rcoulomb = rvdw = 0.62 nm
> pme_order = 6
> epsilon_surface = 0
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