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.war...@monash.edu>
To: GROMACS users <gmx-us...@gromacs.org>
Subject: Re: [gmx-users] Need help creating md.mdp for silica(quartz)?
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

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
When the only tool you own is a hammer, every problem begins to resemble a

Yours sincerely,
Ekatherina O.
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