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

Thomas Schlesier schlesi at uni-mainz.de
Tue Jan 15 14:12:50 CET 2013

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.


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