From: Ingrid Bernardes Santana Martins (ingrid.martins_at_unesp.br)
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.
Greets
Ingrid Bernardes Santana Martins, Msc.
PhD student in Molecular Biophysics.
Ibilce/Unesp
Department of Physics, Room 42.
São José do Rio Preto - SP, Brazil
Em sáb, 25 de mai de 2019 07:52, Adupa Vasista <adupavasista_at_gmail.com>
escreveu:
> *Why Volume of a simulation box ( created either by packmol or NAMD
> plugin-ADD solvation box ) shrinks during Equilibration.*
>
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