[gmx-users] frozen CNT with carbonyls

Mark Abraham Mark.Abraham at anu.edu.au
Mon May 9 15:00:47 CEST 2011

On 9/05/2011 10:43 PM, toby10222224 wrote:

Please use a useful subject line when replying to a digest.

> I mean all the positions of the carbon atoms are invariant during
> mdrun. In the .gro file, carbonyl carbon and oxygen atoms are defined
> as group 'Carbonyl' and the rest every single carbon atom is defined
> as 'CNT'.

A .gro file doesn't have groups.

> For the use of 'freeze groups', the group 'CNT' should be freezed. But
> for group 'Carbonyl', as oxygen atom is allowed to move, it is not
> appropriate to freeze group 'Carbonyl'.

Sure, I think you want a freeze group of all the nanotube carbons, and
all the carbonyl oxygens. make_ndx will allow you make such a union.

> I wonder whether the same atom can be included in two or more groups.
> If it can be, I can ignore the group name defined in the .gro file and
> redefine groups by using command 'make_ndx'. Then I am able to make
> use of index

Groups aren't defined in the coordinate file. If you use a GROMACS
utility that can accept an index file as input, and do not provide one,
then GROMACS generates some standard ones from the coordinate file. In
the case of make_ndx, these are then written out when you quit.

> groups to define an appropriate freezegrp in the .mdp file. All the
> carbon atoms of the CNT (inclduing carbonyl carbon atoms) are supposed
> to be defined as 'CNT', and carbonyl carbon atoms and oxygen oxygens
> are 'Carbonyl'. Group 'CNT' is the freeze group. Is it feasible for
> this idea?

You're in charge... I don't know what external entity is dictating what
you are "supposed" to do :-)


> Thank you!
> 2011-05-09
> ------------------------------------------------------------------------
> toby10222224
> ------------------------------------------------------------------------
> Message: 4
> Date: Mon, 09 May 2011 06:58:04 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] freeze the carbonyl carbon atoms
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4DC7C8BC.5090907 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 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?
> >
> By "fixed," do you mean their positions should be invariant (i.e.
> freeze groups)
> or that their bond lengths should be constrained? If the former, then you
> should be able to make use of index groups to define an appropriate
> freezegrp in
> the .mdp file. If the latter, use "constraints = none" in the .mdp
> file, and
> write a [constraints] directive for the bonds you do wish to be
> constrained.
> -Justin
> > Any suggestions are appreciated!
> > Thank you in advance!
> >
> > 2011-05-09
> > ------------------------------------------------------------------------
> > toby10222224
> >
> -- 
> ========================================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================

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