Re: PMF calculation

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Jul 11 2019 - 15:28:20 CDT

Hello Mahdi, overlapping windows are a necessary condition for a converged
PMF, but are not a sufficient condition. You may very well have covered
the entire region of interest, but if the windows are still equilibrating
the distribution may be smooth, but not be the correct one (yet).

Any error estimate based entirely on the unbiasing method (WHAM, MBAR, etc)
assumes that equilibrium sampling is valid over the entire simulation.
There are some techniques, e.g. DHAM, to try to automatically remove
non-equilibrium effects (as opposed to you manually truncating the
trajectory) but they also assumes that equilibrium is reached before the
end of each window's trajectory. As a corollary, you should take the error
bars generated by those methods with the proverbial grain of salt.

Keep also in mind that the specifics of your system will generate electric
fields that can be longer ranged than you think. After all, I presume you
are not cutting off Coulomb forces at 12 Å but are using Ewald or PME,
right? Only a PMF computed across the entire unit cell should be periodic
at the edges (in the absence of an applied voltage ramp).

Giacomo

On Thu, Jul 11, 2019 at 4:12 PM Mahdi Mousaei <mahdi.mousaei_at_ucalgary.ca>
wrote:

> Thank you for your reply. That’s true, but if we the ion goes from the
> water and end in water, this could happen?
>
>
>
> Best Wishes,
>
> Mahdi
>
>
>
>
> ------------------------------
> *From:* Souvik Sinha <souvik.sinha893_at_gmail.com>
> *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, <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
>>
>>
>>
>>
>>
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Research collaborator, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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