[gmx-users] Confusion Regarding Vacuum

Xavier Periole X.Periole at rug.nl
Mon Nov 26 15:12:49 CET 2007

On Mon, 26 Nov 2007 18:06:46 +0530 (IST)
  csreddy at ncbs.res.in wrote:
> Dear All,
> I am a bit confused regarding  Vacuum. I wanted to do EM in Vacuum. I
> think I can proceed either of the below...
> 1) I create a box (editconf) and place a molecule with out solvent.
> 2) Never create a box, then proceed other steps as usual like EM etc.

you should make sure your mdp file specifies no pbc:
pbc = none

> Can we call 2nd option also a vacuum and what is more appropriate?
> Regards
> Chandu
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XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands

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