[gmx-users] Trajectory viewing by freeing a part

Mark Abraham Mark.Abraham at anu.edu.au
Wed Sep 7 23:03:20 CEST 2011

On 8/09/2011 3:55 AM, Justin A. Lemkul wrote:
> 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.

... and then load two copies of your simulation in your viewer. Show 
only a single frame of this group in one of them, and show only the 
group whose motion is of interest with the other. I doubt this general 
idea will prove very useful, however.


>   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

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