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

Justin Lemkul jalemkul at vt.edu
Thu May 7 14:17:19 CEST 2020

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.


>> 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.


Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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