[gmx-users] restraining Ca2+ ion

jayant james jayant.james at gmail.com
Tue Jan 6 21:50:44 CET 2009

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.
Jayant James

Jayasundar Jayant James

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