[EMAIL PROTECTED] 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
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