Dear Pratibha, The Help page for the tool is here. http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html

Detailed explanations of how to do standard molecular modeling is beyond the scope of this mailing list, however. I can only say to consult a textbook or look in the Methods sections of high-quality papers that present similar types of calculations.

In general, the tool is mean to be relatively simple and does not allow adjusting that many parameters compared to dedicated packages like AMBER, GROMACS, etc. If you want access to more settings and force fields than provided by Chimera, and faster calculations of very long trajectories, you may want to use one of those packages instead.

Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On May 30, 2020, at 6:58 AM, P Srivastava psrivastava@aripune.org wrote:

Dear Chimera Team I Need instructions on how to do MD simulations of Protein-ligand complex using Chimera. Please give me in details. With regards, Pratibha Srivastava