[gmx-users] Longer scale simulations

Ran Friedman ran at hemi.tau.ac.il
Wed Dec 10 13:16:02 CET 2003

Well, that's not very encouraging, but it's better than being wrong!

Thanks a lot,

Berk Hess wrote:

> >Does this approach still confer some advantages compared to normal MD?
> >
> >For example, can I use non-periodic boundary conditions in order to reduce
> >computation time?
> No, it does not.
> If you would want to use non-periodic boundary conditions you would need to
> restrain the outer shell
> of solvent atoms, which introduces artifacts. A boundary layer is required
> to minimize the effect of
> these artifacts.
> In the end it is computationally cheaper to use a periodic system in a
> rhombic dodecahedron box.
> Berk.
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Ran Friedman
Laser laboratory for fast reactions in biology
Department of biochemistry
Faculty of life sciences
Tel-Aviv university

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