[gmx-users] Re: Simulating a large system

[Mark Abraham]

Yes, there's no way to cheat on the explicit electrostatics to reduce cost,
except implicit solvation. The kind of approach used in QM/MM is not useful
for MM/MM! The rate-limiting part is still there.

Mark
On Apr 8, 2013 12:42 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:

> 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
>
> --
>
> ========================================
>
> 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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