PMF calculation

From: Mahdi Mousaei (
Date: Thu Jul 11 2019 - 14:14:37 CDT

Hello to All,

I have used NAMD tutorial for PMF calculation of ion permeation through the ion channel. I have enough sampling due to the overlapping between the histograms. But, I see the asymmetric PMF profile which does not make sense ( I think) since the system is periodic and there is bulk water up and down of the system.
Does anyone have any suggestion why this is happening or any kind of analysis how I can find the reason?

Best Wishes,

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