[gmx-users] number of DD cells

Moeed lecielll at googlemail.com
Fri Mar 4 17:19:26 CET 2011

Hello Justin,


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,

>  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
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Moeed Shahamat
Graduate Student (Materials Modeling Research Group)
McGill University- Department of Chemical Engineering
Montreal, Quebec H3A 2B2, Canada
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110304/55524494/attachment.html>

More information about the gromacs.org_gmx-users mailing list