[Chimera-users] viewing of trajectory

[Elaine Meng]

Hi Atila,
Coincidentally, the answer is almost the same as my previous posting a few minutes ago!  

You can view Gromacs trajectories (.tpr tpology file and .trr portable binary trajectory file).  I believe these formats have changed from time to time with different Gromacs versions, but if you get a recent version of Chimera (version 1.5) it should cover these possibilities.

Trajectories are shown with the  MD Movie tool (start it by choosing Tools... MD/Ensemble Analysis... MD Movie from the Chimera menu).  That gives a file browser for opening trajectory formats.

MD Movie documentation includes a list of the possible formats, and much more about the tool:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>

Also, the following tutorial, part 1, uses MD Movie to view a sample Amber trajectory (data provided along with the tutorial):
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html>

(Part 2 also uses MD Movie, but on different data, an NMR ensemble from the PDB.)

The documentation and tutorials are also included with your download and can be accessed from the Chimera Help menu.  I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Nov 1, 2010, at 3:26 AM, atila petrosian wrote:

> Hi chimera users
> I did simulation of protein by gromacs. I want to see my trajectory during simulation by a viewr other than vmd, such as chimera. 
> How and what files is needed for that? 
> -- 
> Atila Petrosian
> Ph.D. student of BioPhysical Chemistry
> University of Oulu,Finland

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