[gmx-users] Re: Simulating a large system

[Justin Lemkul]

On Mon, Apr 8, 2013 at 5:54 AM, Dr. Vitaly Chaban <vvchaban at gmail.com>wrote:

> If you do not care about the atoms, which are too far away from the region
> of interest, is it not reasonable just to cut that "useless" part? Also,
>

Hear hear. If it's so meaningless, why is it there? ;)


> you may want to look towards implicit solvent simulations.
>
>
Indeed. Or use GPU's. Erik was showing us great performance on a laptop
during the webinar, even using (relatively) cheap consumer-grade cards.
Back to the original point (and as I posted before), even if you freeze
some amount of atoms, you don't gain any performance by doing so.

-Justin

-- 

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

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