AW: recent comparison of NAMD to other MD engines

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Jan 23 2014 - 01:32:54 CST

I do totally agree with Giacomo

 

Norman Geist.

 

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von Giacomo Fiorin
Gesendet: Donnerstag, 23. Januar 2014 03:38
An: Bennion, Brian
Cc: namd-l_at_ks.uiuc.edu
Betreff: Re: namd-l: recent comparison of NAMD to other MD engines

 

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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