Re: ionize (big, big, big system!)

From: Jacob Poehlsgaard (mail_lists_at_hardcoil.net)
Date: Tue Feb 13 2007 - 02:22:23 CST

L. Michel Espinoza-Fonseca wrote:
> Hi,
>
> I've started to use the IONIZE program (kindly provided by Peter
> Freddolino) to add ions to a 2-million atom system. The net charge of
> my system is -3,600 e. I tried to neutralize such system by using 50
> processors (Altix) for 2 days, and nothing happened. Then I tried to
> do it on 100 processors, and the job was killed. Now I'm trying to do
> it with 500 processors (BladeCenter, AMD Opteron) and I'm waiting to
> see if this time the job will be completed. So here is my question: do
> you have any idea of how much time it could take to add such a big
> amount of ions?
>
> Thanks!
>
> Michel
>

  Are there any parameters you can fiddle with?

  I've been using meadionize on largish RNA structures (nothing near
yours, but still..), and I found that the calculation wasn't done in
several days. I then played around a bit with a parameter called "fine
grid resolution". By changing that from 0.25 to 1, my calculation was
done in a few minutes. I did tests on smaller systems with the two
settings, and the results were qualitatively the same.

Jacob
Denmark

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