From: Haohao Fu (fhh2626_at_gmail.com)
Date: Tue Jun 12 2018 - 11:25:39 CDT
The problem is that the reaction coordinate model chosen is too simple to
describe the process. Your definition of RC implies that the rotational
movement and the conformational change of the proteins can be observed in
the time scale of your simulation, which is not true.
Just try to introduce some restraints to reduce the degrees of freedom
(e.g. Orientation、polarPhi and polarTheta colvar) and discuss the effects
of the restraints. See J. Chem. Theory Comput., 2017, 13 (11), 5173–5178
and J. Chem. Theory Comput., 2013, 9 (1), 794–802 for some examples--00000000000021df80056e74516f--
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