From: Ingrid Bernardes Santana Martins (
Date: Sat May 25 2019 - 06:05:29 CDT

Its because the distance of the water molecules when you make the box with
this plug-ins is bigger than Its minimum energy when you think about
Lennard Jones potential and the polarization of the molecules.
A good equilibration is when you "relax" the solvent until it reaches this
minimum, then it shrinks.


Ingrid Bernardes Santana Martins, Msc.
PhD student in Molecular Biophysics.
Department of Physics, Room 42.
São José do Rio Preto - SP, Brazil

Em sáb, 25 de mai de 2019 07:52, Adupa Vasista <>

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

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