[gmx-users] (no subject)
yang.he at mavs.uta.edu
Sun Apr 19 22:15:09 CEST 2009
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:
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.
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