Am 15.01.2013 14:17, schrieb gmx-users-requ...@gromacs.org:
On 1/15/13 8:12 AM, Thomas Schlesier wrote:
>Am 15.01.2013 12:52, schriebgmx-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
This makes sense. Thanks for the answer.
Thomas
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