[gmx-users] Confusion Regarding Vacuum

Mark Abraham Mark.Abraham at anu.edu.au
Tue Nov 27 02:36:53 CET 2007

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.
> Can we call 2nd option also a vacuum and what is more appropriate?

A simulation in vacuo requires that you don't put a solvent in.
A simulation with PBC requires that you choose the appropriate pbc 
option in your .mdp file, and also choose a sensible box size, e.g. with 

These two are independent choices.


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