[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:
> [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.


> I hope what  I said is clear to you all and I really appreciate your any suggestions.
> Yang
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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