On 1/15/13 8:12 AM, Thomas Schlesier wrote:
Am 15.01.2013 12:52, schrieb gmx-users-requ...@gromacs.org:
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.


If the ion is structurally bound to the protein, I think it makes more sense to couple it to the protein rather than the solvent since the dynamics of the two species are more tightly linked. It's not a free-floating ion like others that might be in solution.

-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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