From: Axel Kohlmeyer (
Date: Sat May 25 2019 - 06:17:28 CDT

On Sat, May 25, 2019 at 6:51 AM Adupa Vasista <>

> *Why Volume of a simulation box ( created either by packmol or NAMD
> plugin-ADD solvation box ) shrinks during Equilibration.*

because you need to leave extra space at the periodic boundaries and
between solvent and solute to avoid overlap of atoms. during
equilibration, these interfaces "heal" and then you either have a shrinking
box, when using variable cell MD or you'll see a small vacuum bubble
forming, when using constant volume MD.


Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

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