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

Mark Abraham Mark.Abraham at anu.edu.au
Mon May 9 15:02:56 CEST 2011

On 9/05/2011 10:55 PM, toby10222224 wrote:
> I intend to apply an electric filed on the whole system and the
> possitive oxygen will be certainly affected.

Please give full descriptions the first time... otherwise everyone's
time gets wasted.

Under such a field, surely the carbonyl carbon atoms will also be
affected - if the oxygen has a partial charge to be affected by the
field, so must the carbon. Whether or not the other carbon atoms are
charged, they'll be affected through the bonds to the first carbon. A
rigid CNT seems to make little sense here.


> 2011-05-09
> ------------------------------------------------------------------------
> toby10222224
> ------------------------------------------------------------------------
> 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.
> Mark
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