[gmx-users] MD Simulation of Calcium with protein

Justin Lemkul jalemkul at vt.edu
Tue Jan 15 12:05:57 CET 2013

On 1/15/13 5:49 AM, Devika N T wrote:
> HI
> I would like to know the protocol to be followed for performing MD
> simulation
> for calcium with protein (Calmodulin)
> Can I follow the same protocol which is followed for a protein?

Probably, as long as the force field you choose can deal with calcium (most 
can).  The only special thing to do would be to couple the Ca2+ ions to the 
protein for the purpose of temperature coupling, which requires a custom index 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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