From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Nov 28 2012 - 10:07:02 CST
On Wed, Nov 28, 2012 at 4:57 PM, Aron Broom <broomsday_at_gmail.com> wrote:
> Just checked some simulations, and I'm only really seeing an ~5% speed drop
> over 50,000,000 steps with implicit solvent. That is also using
i didn't say that *all* implicit solvent simulations.
were affected, but rather simulation where the
number of neighbors is changing. that may or
may not be with implicit solvent. it is just more likely.
you can have it also when you have, say, a liquid/gas
system where you heat up the liquid to evaporate
(the simulation gets faster this time).
when doing self assembly with implicit solvent, the
number of neighbors per atom increases and the
simulation (GPU or CPU) will slow down. also in the
case depicted in this movie the simulation speed
varies significantly, depending on where exactly
the buckyballs are located.
http://youtu.be/JGz5oFR71jA
axel.
> metadynamics, which could slow things down over time also.
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
>
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy.
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