Am 15.01.2013 12:52, schrieb [email protected]:
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: Why would you couple the calcium ion with the protein and not
with the water / solvent? Just being interested. Thought commonly one
couples the ions with the solvent.
Thomas
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