Charged methyl guanidine is used as a model ion to study the transmembrane permeation of ions.With a widely applied reaction coordinate, our umbrella sampling discovers a dilemma in obtaining the transition trajectory and the potential of mean force-significant finite-size effect in small systems and serious hysteresis in large systems.This suggests the importance of re-examining the validity of the transition trajectory and the potential of mean force obtained in previous works.In this work, a novel reaction coordinate is designed to acquire a continuous trajectory of the permeation process in a large simulation system.This continuous trajectory demonstrates the presence of a water pore at the saddle state which is not clearly observed in previous works.With the presence of the water pore, the energy barrier is shown to be significantly decreased.