[gmx-users] Re: Simulating a large system

Justin Lemkul jalemkul at vt.edu
Mon Apr 8 13:41:19 CEST 2013

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)


More information about the gromacs.org_gmx-users mailing list