[gmx-users] Re: MD Simulation of Calcium with protein

[Thomas Schlesier]

Am 15.01.2013 14:17, schrieb gmx-users-request at gromacs.org:
> On 1/15/13 8:12 AM, Thomas Schlesier wrote:
>> >Am 15.01.2013 12:52, schriebgmx-users-request at 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