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

Justin Lemkul jalemkul at vt.edu
Tue Jan 15 14:15:41 CET 2013

On 1/15/13 8:12 AM, Thomas Schlesier wrote:
> Am 15.01.2013 12:52, schrieb gmx-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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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