[gmx-users] calcium diffuses away from the protein during MD

[Mark Abraham]

On 4/03/2011 4:55 PM, Sunita Patel wrote:
> Dear Users,
>
> I performed MD simulation on a calcium binding protein with bound calcium
> starting from the crystal structure using gromos96 forcefield with explicit
> solvent with NVT ensembles. I performed energy minimization of calcium bound
> protein with water and following this position restraint molecular dynamics
> was performed. Subsequently, MD was performed on the system. In a less
> than 100 ps the calcium ion diffuse away from protein. However, in the
> experiment (NMR and X-ray)the protein is stable in calcium bound form.
>
> What could be the reason for this?

Either your model does not provide a site that binds calcium, or you ran 
into a periodicity effect (unlikely). Check the literature for 
successful approaches for binding metal ions.

Mark