[gmx-users] PBC in a closed box.
Rodney Versace Babilonia
rversace at ccny.cuny.edu
Sat Aug 8 18:20:55 CEST 2015
Thanks for you answer, I didn't think about it, but actually a spherical droplet will be more ideal to this project than a cubic box.
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of André Farias de Moura <moura at ufscar.br>
Sent: Tuesday, August 4, 2015 1:59 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] PBC in a closed box.
choosing the electrostatic treatment seems to be the least of your
problems: once you turn off the PBC, water molecules will coalesce into a
spherical droplet in order to minimize the surface energy, so you first
have to ask yourself if a nanometric water droplet suits your needs. Not a
simulation issue, rather a surface chemistry fact.
On Tue, Aug 4, 2015 at 2:24 PM, Rodney Versace Babilonia <
rversace at ccny.cuny.edu> wrote:
> Hi all,
> I am trying to simulate the effusion process of water through hole in a
> very thin film. The film is partitioning the water box, I wish to count the
> numbers of waters before and after the simulation in each compartment, but
> I am afraid that the use of periodic boundary conditions will make waters
> from one side going to the other side through the boundaries and that
> affect my counting, in case I turn off the PBC, what kind of electrostatic
> treatment should I use?
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Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
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