[gmx-users] Trajectory viewing by freeing a part

Justin A. Lemkul jalemkul at vt.edu
Wed Sep 7 19:55:49 CEST 2011

Ragothaman Yennamalli wrote:
> Hi,
> While viewing a trajectory I am trying to see how a particular part or 
> group is behaving, while keeping the rest frozen (I dont want them to 
> move). For example, in a two domain protein keeping one domain frozen 
> and seeing the other domain movement or in a protein ligand complex 
> keeing the protein frozen and seeing the movement of the ligand. I tried 
> -center in trjconv and selected the group that I need to center. Any 
> other suggestions?

Use trjconv -fit rot+trans with a custom index group of whatever you'd like to 
keep (somewhat) fixed.  You cannot fix any group's position with trjconv; you 
can only remove periodicity and to least-squares fitting to get a smooth trajectory.



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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