Hi Justin, In fact, I just get the error. I have tried to use the freezegroup but it seems that it only work for the whole group not certain atoms in the whole group.
Yang ________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Sunday, April 19, 2009 1:42 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] (no subject) He, Yang wrote: > Hi all users, > > I am trying to create the ndx file to define the atoms which I want to add > the position restraints to. What I create is like this: > > [God] > 21 22 > [Bad] > 61 62 > > And I have defined the atom numbering 21, 22, 61,62 in gro file like this : > > 2MOM bT 21 0.805 1.330 3.914 > 2MOM bT 22 0.448 1.572 3.576 > > 4ICE bT 61 0.805 4.330 3.914 > 4ICE bT 62 0.448 4.572 3.576 > > I know this may cause error cause I just define one atoms in two groups. I > just want to freeze only two atoms in the group[MOM](A single DNA strand) > while keep the other atoms in this group move freely , Meanwhile, the two > frozen atoms have a bond connection with the other atoms in this [MOM]group > ,which is assumed that this single DNA strand will be fixed because of the > two fixed atoms and the other atoms will move freely at the same time. I > wonder how I can define this position restraints in gromacs . > Are you assuming an error, or have you tried it and actually received an error? Use these groups as the "freezegrps" in the .mdp file and try it. It should be fine. -Justin > I hope what I said is clear to you all and I really appreciate your any > suggestions. > > Yang > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- ======================================== 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 ======================================== _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php