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.
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
========================================
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