] Need help creating md.mdp for silica(quartz)?
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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
2020 14:14:41 +0200
From: Debashish Banerjee
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Need help creating md.mdp for silica(quartz)?
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Hello Ekatherina, I did not reach a point in my simulations where I
have
used free
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 War
’t need them to move.
Freezing is very artificial and leads to unphysical collisions. Avoid if
at all possible.
-Justin
Message: 4
Date: Tue, 5 May 2020 09:12:51 +1000
From: Dallas Warren
To: GROMACS users
Subject: Re: [gmx-users] Need help creating md.mdp for silica(quartz)?
Message-ID:
Cont
ructure (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
> > To: GROMACS users
&g
To: GROMACS users
Subject: Re: [gmx-users] Need help creating md.mdp for silica(quartz)?
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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 f
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
