[gmx-users] number of DD cells

[Justin A. Lemkul]

Justin A. Lemkul wrote:
> 
> 
> Moeed wrote:
>> Hello Justin,
>>
>> Thanks.
>>
>> 1- I changed the setting below because of the note I used to get:
>>
>> NOTE 1 [file aminoacids.dat, line 1]:
>>   The optimal PME mesh load for parallel simulations is below 0.5
>>   and for highly parallel simulations between 0.25 and 0.33,
>>   for higher performance, increase the cut-off and the PME grid spacing
>>
> 
> I'm guessing this pertains to your "expanded" system, before you've 
> obtained an optimum density?  If so, you're only going to be losing 
> performance for some simulations, but not all.  It also depends on just 
> how bad the load imbalance is.  If you can set it such that you can 
> easily specify -npme to match the PP:PME ratio, then you shouldn't be 
> hurt too badly.
> 
>> Also, earlier on I read one of your messages about the trade off 
>> between accuracy and speed for this setting and that no systematic 
>> study has been done how exactly accuracy is changing. I actually need 
>> to work with systems with 40 000 atoms or even more and electrostatics 
>> slows down my runs to a great extent. Can you please give an idea on 
>> to what extent the accuracy affects the result say for 
>> fourierspacing      =  0.2 . I mean it affects second decimal or...? I 
>> need to go for a setting which 
> 
> You may want to look into g_tune_pme.  It should provide this sort of 
> information.  There was also some discussion about this just a few weeks 
> ago, but I don't have the time or desire to go rooting through the list 
> archive at the moment.
> 

Sorry, that should be g_pme_error.

-Justin

>> speeds up calculations as much as possible while being reasonable. How 
>> would you deal with this? What value would you pick?
>>
> 
> Ideally, one that is well-tested and that you can defend to a critical 
> audience.  If 0.12 is standard, and I have no desire to experiment with 
> accuracy, I tend to stick with that :)
> 
> -Justin
> 
>> Thank you,
>> moeed
>>
>>
>>         fourierspacing      =  0.3               
>>
>>     You're setting yourself up for inaccurate PME calculations with
>>     this.  Use 0.1 - 0.12 unless you've got some compelling reason to
>>     decrease your accuracy.
>>
>>     -Justin
>>
>>     --     ========================================
>>
>>     Justin A. Lemkul
>>     Ph.D. Candidate
>>     ICTAS Doctoral Scholar
>>     MILES-IGERT Trainee
>>     Department of Biochemistry
>>     Virginia Tech
>>     Blacksburg, VA
>>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
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>>
>>
>>
>> -- 
>> Moeed Shahamat
>> Graduate Student (Materials Modeling Research Group)
>> McGill University- Department of Chemical Engineering
>> Montreal, Quebec H3A 2B2, Canada
>> Web:http://mmrg.chemeng.mcgill.ca/pages/current-group-members/moeed-shahamat.php 
>>
>> Web:http://mmrg.chemeng.mcgill.ca/
>>
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================