[gmx-users] Freezing a portion of a protein during simulation

Justin A. Lemkul jalemkul at vt.edu
Fri Apr 23 14:07:31 CEST 2010

Anirban Ghosh wrote:
> Hi ALL,
> I want to do a MD simulation by restraining (freezing) the helical 
> portions and allowing only the loop regions to move. I tried doing this 
> by applying heavy restrain on the helical residues by generating a .itp 
> file with the "genrestr" command with an index file containing the 
> desired residue numbers. However during the simulation I am finding that 
> the entire protein is moving. Am I doing anything wrong? Or is there any 
> other way to freeze a portion of a protein? Any suggestion is welcome. 
> thanks a lot in advance.

If your protein is still moving, then you aren't correctly applying your 
position restraints.  Without seeing your topology and .mdp file, there's no way 
to know what you're doing wrong.

You can also use the freezegrps option in the .mdp file, but then you also have 
to make sure you're using the appropriate energygrp_excl, etc.  It is generally 
much easier to apply position restraints.


> Regards,
> Anirban


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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