From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat May 25 2019 - 06:17:28 CDT
On Sat, May 25, 2019 at 6:51 AM Adupa Vasista <adupavasista_at_gmail.com>
> *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 akohlmey_at_gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy.
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