Dear all,
I want to do some molecular dynamic simulation for a protein to verify the hypothesis that the side chain of W286 in the protein can rotate freely. The protein was solvated in TIP3P water and 9 Na+ as counterions were added to neutralize the charge. But one Na+ was placed colsely to the W286, and when I checked the trajectory of the simulation I found that the side chain of W286 was nearly freezed via the pi-π interaction between the benzene ring of W286 and the Na+, so the simulation does not do any help .
What I want to ask is that can I move the Na+ a little further from W286 while still keeping the system neutralized so that the counterion does not limit the rotation of side chian ? If I can, how to do it ? if not , is there anyway to solve the problem?
-sun
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Received on Sun Feb 17 2013 - 11:00:02 PST
