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

[Debashish Banerjee]

Hello Justin, so I believe it's just pbc visualization stuff going on
then.. okay.. yes you can do it then from trjconv .

Regards,
Debashish

On Thu, 7 May 2020, 14:14 Debashish Banerjee, <deb.aerospace at gmail.com>
wrote:

> Hello Ekatherina, I did not reach a point in my simulations where I have
> used freeze command, but I think for your case, can't you put a position
> constraint on your quartz layer. In that case, you just have to create an
> index file having quartz in the group and then you can put postion
> restraints on them in x,y,z by putting force constant of [1000 1000 1000]
> so that the layer doesn't move.
>
> Regards,
> Debashish
>
>
>
>
>
> On Thu, 7 May 2020, 10:28 Ekatherina O, <oeg at isc-ras.ru> 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?
>> 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.
>>
>> > Message: 4
>> > Date: Tue, 5 May 2020 09:12:51 +1000
>> > From: Dallas Warren <dallas.warren at monash.edu>
>> > To: GROMACS users <gmx-users at gromacs.org>
>> > Subject: Re: [gmx-users] Need help creating md.mdp for silica(quartz)?
>> > Message-ID:
>> >       <CAOv1qzY3iYKVgOTJRb=_
>> dTXkx86OhDbsDYjg2MA2+Tpa8GEetA at mail.gmail.com>
>> > Content-Type: text/plain; charset="UTF-8"
>> >
>> > 1/ it means that between the original coordinate file loaded with vmd
>> > and
>> > the frame you are looking at there from the trajectory file, those
>> > atoms
>> > have moved across the periodic boundary and vmd is still drawing the
>> > bond
>> > between them. vmd knows nothing about bonds, it guesses where the bonds
>> > should be and maintains them between those atoms when viewing a
>> > trajectory.
>> > If looking to make a nice looking animation simply using gmx trjconv to
>> > move the layer into the center of the box. Otherwise use a viewing
>> > method
>> > in vmd that doesn't draw the bonds i.e. VDW, Points or one that redraws
>> > each frame i.e. DynamicBonds
>> >
>> > 2/ where the simulation box is located is entirely arbitrary. So if it
>> > is
>> > not in the location you want then use gmx trjconv to move it to where
>> > you
>> > want it to be.
>> >
>> > All these things you are seeing here are artifacts of the periodic
>> > boundary
>> > condition:
>> >
>> http://manual.gromacs.org/documentation/current/user-guide/terminology.html#gmx-pbc
>> >
>> >
>> > Catch ya,
>> >
>> > Dr. Dallas Warren
>> > Drug Delivery, Disposition and Dynamics
>> > Monash Institute of Pharmaceutical Sciences, Monash University
>> > 381 Royal Parade, Parkville VIC 3052
>> > dallas.warren at monash.edu
>> > ---------------------------------
>> > When the only tool you own is a hammer, every problem begins to
>> > resemble a
>> > nail.
>>
>> --
>> Yours sincerely,
>> Ekatherina O.
>> oeg at isc-ras.ru
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>
>