[gmx-users] restraining Ca2+ ion

Mark Abraham Mark.Abraham at anu.edu.au
Tue Jan 6 23:43:25 CET 2009

jayant james wrote:
> Hi!
> I have been performing MD simulations of a protein which has 3 ca2+ 
> ions. I find that after 3ns of simulations the ca2+ ions start to drift 
> away. So what would be a good strategy to have the ca2+ in place during 
> the simulations. I would  prefer not to use position restraining as this 
> would pin the ca2+ in space hindering the spacial movement of that 
> particular area!! but I am wondering if distance restraining of the ca2+ 
> to the adjacent residues would be fine? or is there any other/better 
> strategy? Awaiting your suggestions.

This is one of the purposes of distance restraints. Better would be a 
proper model for protein-bound calcium ions. Also, a poor-quality 
electrostatic treatment could be the source of the problem (e.g. a 
cut-off shorter than the distances to nearby negative (partial) charges).


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