[gmx-users] Re: freeze the carbonyl carbon atoms

toby10222224 toby10222224 at sina.com
Mon May 9 14:55:56 CEST 2011

I intend to apply an electric filed on the whole system and the possitive oxygen will be certainly affected.



Message: 5
Date: Mon, 09 May 2011 22:38:48 +1000
From: Mark Abraham <Mark.Abraham at anu.edu.au>
Subject: Re: [gmx-users] freeze the carbonyl carbon atoms
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4DC7E058.10501 at anu.edu.au>
Content-Type: text/plain; charset="iso-8859-1"
On 9/05/2011 5:23 PM, toby10222224 wrote:
> Hi:
> I have a carbon nanotube (CNT) and several carbonly groups (C=O). 
> Meanwhile the carbonly carbon atoms are part of the CNT. That is to 
> say an oxygen atom is attached to one carbon atom of the CNT to form a 
> carbonyl group. All the carbon atoms are supposed to be fixed, while 
> carbonyl carbon and oxygen atoms are supposed to have bond 
> interactions. I can freeze the rest carbon atoms of the CNT, but how 
> to deal with the carbonly atoms?
Well if you're prepared to model the CNT frozen, why not freeze the 
oxygen bound to it? Anything else sounds like a recipe for more trouble.
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