[gmx-users] Need help creating md.mdp for silica(quartz)?

Ekatherina O oeg at isc-ras.ru
Fri May 8 09:15:28 CEST 2020

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 <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Need help creating md.mdp for silica(quartz)?
> Message-ID: <cc73a001-d4b1-c470-c0a2-5f7bdc2aa493 at 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.
oeg at isc-ras.ru

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