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

XAvier Periole x.periole at rug.nl
Fri Mar 4 08:49:12 CET 2011

It is unfortunately often that cations on their binding sites in proteins are not stable. Either the site reorganize or the ion leaves. 

The problem is that ions parameters and especially double charged ones are difficult to parameterize. 

It is often that people use additional restrains (harmonic bonds, weak compared to regular ones) to maintain the ion bound. 


On Mar 4, 2011, at 6:55, Sunita Patel <sunita at mailhost.tifr.res.in> 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?
> How can this problem be fixed?
> Thanks.
> Sunita
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