The accuracy of FEP calculation

Date: Thu Feb 11 2010 - 09:58:20 CST

Hi all,

I am using FEP to calculate the binding energy of Na ion inside the
protein. I did not put any restraint on the ion and observed that later on
this ion moved away from the binding site. This ion is supposed to
disappear finally. Should ion's moving away from the binding site affect
the binding energy? I think I may need to restrain it. Any suggestion?



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