[gmx-users] number of DD cells

[Moeed]

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

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 speeds up
calculations as much as possible while being reasonable. How would you deal
with this? What value would you pick?

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 | (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/
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