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

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 (harm

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

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 wa

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

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 m