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

Sunita Patel sunita at mailhost.tifr.res.in
Fri Mar 4 06:55:42 CET 2011

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?



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