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)?
Message-ID:
<CAOv1qzY3iYKVgOTJRb=_dtxkx86ohdbsdyjg2ma2+tpa8ge...@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.war...@monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to
resemble a
nail.
--
Yours sincerely,
Ekatherina O.
o...@isc-ras.ru
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