[gmx-users] (no subject)

He, Yang 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:

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 .

I hope what  I said is clear to you all and I really appreciate your any suggestions.


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