[gmx-users] (no subject)
Justin A. Lemkul
jalemkul at vt.edu
Sun Apr 19 22:42:14 CEST 2009
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:
> 21 22
> 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
> I hope what I said is clear to you all and I really appreciate your any suggestions.
> gmx-users mailing list gmx-users at gromacs.org
> 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users