Re:

From: Ingrid Bernardes Santana Martins (ingrid.martins_at_unesp.br)
Date: Sat May 25 2019 - 06:49:03 CDT

Thanks for your response, I learned it wrond and tought it wrong all this
time.
I tought it was like this in The energy minimization

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 08:24, Axel Kohlmeyer <akohlmey_at_gmail.com>
escreveu:

>
>
> On Sat, May 25, 2019 at 7:07 AM Ingrid Bernardes Santana Martins <
> ingrid.martins_at_unesp.br> 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.
>
> axel.
>
>
>
>>
>> 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.*
>>>
>>
>
> --
> 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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