[gmx-users] Confusion Regarding Vacuum

[Mark Abraham]

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 
editconf.

These two are independent choices.

Mark