Re: PMF calculation

From: Souvik Sinha (souvik.sinha893_at_gmail.com)
Date: Thu Jul 11 2019 - 15:08:08 CDT

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, <mahdi.mousaei_at_ucalgary.ca> 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,
>
> Mahdi
>
>
>
>
>

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