[gmx-users] frezzing a bond

Justin A. Lemkul jalemkul at vt.edu
Sat Jul 17 02:19:45 CEST 2010

Nilesh Dhumal wrote:
> Hello,
> I am trying to freeze a bond (3.5 A) in my system.  I used the index file
> to define group and I added this two lines in my .mdp file.
> freezegrps         = PA NE
> freezedim   = Y Y Y Y Y Y
> I used g_dist to verify the distance between the freezing atoms and it
> turned out 3.9 A. I checked my .itp also (distance is 3.5).
> How can I freeze a bond?

How about distance restraints instead?  Seems like an applicable situation.  Or, 
just define the actual bond in your topology and use constraints.


> Nilesh


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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