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 . 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
