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
group.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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