Re: SHAKE Tolerance and Performance

From: Aron Broom (
Date: Thu Mar 01 2012 - 11:28:45 CST

Hi Nicholas,

Thanks a lot for the reply. I did actually have useSettle on, but it turns
out the difference was something far less exciting, and much more
embarrassing. I had been quite careless in copy and pasting part of
another config file and had managed to comment out the PME section, which
meant I wasn't using periodic conditions or PME at all. Since I was only
doing short benchmarking simulations I never ended up looking at the actual
trajectories to catch this, and the barostat didn't complain about not
having periodic conditions (although they sure helped it run much faster).
So my whole message about SHAKE should be ignored, as checking it properly
gives me the same result that you saw, a very minor improvement.

Sadly though it also means that AMBER is back to running much faster on the
GPU with the same settings (~1.7x faster, and that's when taking advantage
of NAMD's multiple timestepping of 2fs, 2fs, 6fs, if you match AMBER's 2fs
for everything, AMBER ends up being ~3x faster, but maybe some of that
comes from differences in single vs. double precision). Oh well, quite
depressing really, but thanks again for the reply.


On Thu, Mar 1, 2012 at 4:16 AM, Nicholas M Glykos <>wrote:

> Hi Aron,
> > At some point, in playing around with something for a particular system,
> I
> > discovered that in AMBER when one uses SHAKE and a 2fs timestep, you get
> > pretty close to a 100% boost in performance. In NAMD, you generally get
> > something in range of 15-30%, and since I'd been doing most of my work
> with
> > SHAKE, that seemed to explain the difference.
> I believe that most people leave the default for 'useSettle' (which is on)
> and, thus, use SETTLE for waters. The implication is that for most
> applications the performance difference by changing the tolerance will be
> much lower than the 70% you implied (I did a quick check with a node
> equipped with a GTX295 card and the difference was only ~3% faster with a
> tolerance of 1.0e-5).
> My twocents,
> Nicholas
> --
> Nicholas M. Glykos, Department of Molecular Biology
> and Genetics, Democritus University of Thrace, University Campus,
> Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
> Ext.77620, Tel (lab) +302551030615,

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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