RE: PMF calculation

From: Mahdi Mousaei (
Date: Thu Jul 11 2019 - 15:11:32 CDT

Thank you for your reply. Thatís true, but if we the ion goes from the water and end in water, this could happen?

Best Wishes,

From: Souvik Sinha <>
Sent: Thursday, July 11, 2019 1:08:08 PM
To: NAMD list; Mahdi Mousaei
Subject: Re: namd-l: PMF calculation

The entry and exit of the ion channel may have different residual distribution which may cause different interaction of the ion with the pore residues, thus the asymmetric PMF along the channel axis. Dose it make sense?

On Fri, 12 Jul 2019, 00:46 Mahdi Mousaei, <<>> wrote:
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,

This archive was generated by hypermail 2.1.6 : Thu Dec 31 2020 - 23:17:11 CST