From: Thomas Evangelidis (tevang3_at_gmail.com)
Date: Wed Nov 28 2012 - 16:44:36 CST
On 29 November 2012 00:09, Thomas Evangelidis <tevang3_at_gmail.com> wrote:
> Hello,
>
> 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:
>
> cutoff 14.0
> switchdist 13.0
> pairlistdist 16.0
>
> 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!
>
> I think I made a mistake hear, have left the above parameters unchanged.
This time I set them to:
cutoff 999
switching off
#switchdist 13.0
#pairlistdist 16.0
staticAtomAssignment yes
and got 0.0137201 s/step which is not bad either.
> many thanks for your constructive comments,
> Thomas
>
>
>
>
> 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.
>>
>> ~Aron
>>
>> P.S.
>>
>> 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
>>> 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.
>>>
>>
>>
>>
>> --
>> 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/
>
>
>
>
--
======================================================================
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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