From: Axel Kohlmeyer (
Date: Sat May 25 2019 - 06:24:15 CDT

On Sat, May 25, 2019 at 7:07 AM Ingrid Bernardes Santana Martins <> wrote:

> 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.

equilibration is not looking for the (potential) energy minimum, but for a
_balance_ (hence the name) between potential energy and kinetic energy.
energy minimization is looking for the potential energy minimum, but that
will take you away from equilibrium. you often do a minimization anyway,
since you may have locally high potential energy, so the minimization will
remove those spots and thus make it easier to have a stable running MD.
most tools to solvate molecules use pre-equilibrated solvent boxes, so
those molecules are in equilibrium with each other already. however, if you
cut the box to fit a specific length or cut a hole for the solute, or both,
you leave extra space to avoid overlapping atoms (and thus a crashing
simulation because of that).

now, if you start from a box of a grid solvent molecules at random
orientation, you typically will have a lower density as in equilibrium, but
- again - the main motivation for that is to avoid overlapping atoms.


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

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

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