Re: recent comparison of NAMD to other MD engines

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Jan 22 2014 - 20:38:29 CST

Without reading the paper in detail (I only saw Figures 6-8), I think you
should try to obtain the original input files used for each program, in
particular the cutoffs, PME grid resolution, time steps, etc.

It is not rare to find that the input files do not necessarily have the
same parameters: I once saw a comparison between program X running with a 8
cutoff and 1.5 Ewald grid, vs. program Y running with a 12 cutoff and
0.8 Ewald grid. I'd leave it up to you to judge the accuracy of such
comparison.

Ultimately, benchmarks should be considered as any other scientific data:
they must be reproducible.

Giacomo

On Wed, Jan 22, 2014 at 7:22 PM, Bennion, Brian <Bennion1_at_llnl.gov> wrote:

> Hello,
>
>
>
> Based on this recent publication
> http://onlinelibrary.wiley.com/doi/10.1002/jcc.23501/abstract
>
> NAMD2.9 stumbles compared with gromacs and an improved version of charmm
> on a large system (465404 atoms and 500 cores).
>
> Any ideas as to the cause of this dramatic difference in speed between 256
> and 400 cores?
>
>
>
> Brian
>
>
>

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