[Chimera-users] MD simulation

Elaine Meng meng at cgl.ucsf.edu
Mon Jan 16 10:17:04 PST 2012

Dear Suda,
Sorry, Chimera does not do MD simulations currently -- instead its MD Movie tool can be used to view and analyze MD trajectories output from several other programs (Amber, Gromacs, etc.):

Examples of using MD Movie with already-calculated trajectories or ensembles are given in this tutorial:

Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 15, 2012, at 11:36 AM, Suda Ravindran wrote:

> Dear list,
> I am new to MD simulation, so please forgive me.. I am working on membrane proteins and would like to know if Chimera can be used to do MD simulation right from scratch. If yes, can you guide me on how to do it for a protein in (a) free state (i.,e., only with the protein of interest) and (b) protein docked with its ligand... please help me out..!! 
> Best,
> Suda

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