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 :-) Mark > Thank you! > 2011-05-09 > ------------------------------------------------------------------------ > toby10222224 > ------------------------------------------------------------------------ > Message: 4 > Date: Mon, 09 May 2011 06:58:04 -0400 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] freeze the carbonyl carbon atoms > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4dc7c8bc.5090...@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 > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > ========================================
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
