From: Thomas Evangelidis (tevang3_at_gmail.com)
Date: Wed Nov 28 2012 - 16:09:10 CST
My system consists of 2796 atoms. Although there are parts of the protein
that fluctuate, the speed drops progressively, namely there is no peak in
the performance during any time interval. Therefore I don't think it's a
consequence of the changes in the number of neighbours.
However, when I resume the simulation, the initial speed is approximately
the final speed of the previous simulation part. Therefore, it has to do
with the changes in my system. I must run a plain CPU simulation and see if
the performance drops too. Axel, can you please elaborate what you mean
with "the system becomes more disordered over time"?
Indeed +mergegrids provides a performance boost, from 0.0214802 s/step to
0.0171684 s/step. I also use a cutoff with no PBC:
When I turn staticAtomAssignment on together with +mergegrids I see a
robust speed up, 0.0111643 s/step. Essentially with these two parameter
tweaks the performance has doubled!
many thanks for your constructive comments,
On 28 November 2012 18:40, Aron Broom <broomsday_at_gmail.com> wrote:
> right. So based on all of that, if the number of atoms is smallish and
> you're not intending to use a cutoff, the "staticAtomAssignment yes" option
> in NAMD is worthwhile, otherwise you just have to suffer I suppose. With a
> single protein of ~2000 atoms, I see about the same simulation speed in
> implicit solvent using either a 12 angstrom cutoff, or no cutoff with
> staticAtomAssignment on an M2070 GPU. Not sure to what system size that
> still holds true.
> That's a neat video.
> On Wed, Nov 28, 2012 at 11:07 AM, Axel Kohlmeyer <akohlmey_at_gmail.com>wrote:
>> 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
>> > 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.
>> > 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.
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
-- ====================================================================== Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tevang_at_pharm.uoa.gr tevang3_at_gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/
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