It always show the common error "Invalid order for directive defaults".I suppose it is because I have defined an atom belonging to two groups . What do you mean "by freezing subgroups of atoms within a molecule" ? I just wonder how to make it ?Can you give me some examples?
Thank you very much. Yang ________________________________________ From: [email protected] [[email protected]] On Behalf Of Justin A. Lemkul [[email protected]] Sent: Sunday, April 19, 2009 3:47 PM To: Gromacs Users' List Subject: Re: [gmx-users] (no subject) He, Yang wrote: > 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. > Alright, so what's the error? You should be able to freeze subgroups of atoms within a molecule; I've done it several times in different instances. -Justin > Yang > ________________________________________ > From: [email protected] [[email protected]] On Behalf > Of Justin A. Lemkul [[email protected]] > 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 [email protected] >> 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 [email protected]. >> 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 [email protected] > 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 [email protected]. > 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 [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
