[gmx-users] Re: gmx-users Digest, Vol 85, Issue 67

toby10222224 toby10222224 at sina.com
Mon May 9 14:43:14 CEST 2011

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'. 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'. 
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 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?
Thank you!



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.
> 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
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