Hello  Justin Lemkul,
Thank you for the suggestions. I understood and already tried using transforms with trjconv. The picture got better.


Message: 4
Date: Thu, 7 May 2020 08:17:06 -0400
From: Justin Lemkul <jalem...@vt.edu>
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Need help creating md.mdp for silica(quartz)?
Message-ID: <cc73a001-d4b1-c470-c0a2-5f7bdc2aa...@vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed

On 5/7/20 4:24 AM, Ekatherina O wrote:
Hello Dr. Dallas Warren,
Thank you for the suggestions.

But this does not solve the problem of the movement of atoms of quartz
layers (upper and lower) located at the borders of the box. I would
like the quartz layers to remain intact during the modeling process,
i.e. atoms did not move and the initial structure was disturbed. How
can I solve this problem?

I will reiterate what Dallas has said - if you have atoms that are
exactly at the bottom of the box, they effectively *are* the boundary
and therefore can seem to "jump" back and forth. This has no implication
whatsoever on the physics, just visualization. You can "fix" the issue
after the fact with trjconv.

Can I freeze structure (atoms)? Since with a further increase in
simulation time, I observe the movement of quartz layers in the box. I
don?t need them to move.

Freezing is very artificial and leads to unphysical collisions. Avoid if
at all possible.

Yours sincerely,
Ekatherina O.
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