Re: [External Email] Re: Cations spontaneous binding pathway with PMF calculation?

From: Jiali Wang (
Date: Fri Jan 31 2020 - 10:14:59 CST

Thank you Giacomo.
The reason I asked this because I asked one professor before. He told me
it's unnecessary to do PMF calculations under a spontaneous pathway. He
told me PMF energy barrier should be 0. By your response, it's probably
more complex than a simple result, energy barrier with 0.

On Fri, Jan 31, 2020 at 10:22 AM Giacomo Fiorin <>

> Hello Jiali, I am not sure that this is a NAMD question (probably why you
> didn't get an answer the first time).
> PMFs can be computed under many conditions, even from experimental data.
> For different condensed-phase systems, PMFs can have very different
> magnitudes without being zero. PMFs with very high values are generally
> difficult to compute in MD simulations, because the probability of the
> corresponding states is exponentially small. I assume that you are aware
> of this: otherwise, please read up.
> More specific advice can only be given by those working with you on your
> project. When you have a technical question that is not covered in the
> manuals, that's what the mailing list is for.
> Giacomo
> On Fri, Jan 31, 2020 at 9:43 AM Jiali Wang <>
> wrote:
>> Dear NAMD users,
>> I am confused about the energy barrier calculation in the
>> spontaneous binding process. If a Cation spontaneous binding pathway means
>> in this pathway potential mean force is 0? or does it has meaning to do
>> PMF calculations if MD simulation already shows the binding pathway?
>> Thank you!!
>> Jiali
> --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Research collaborator, National Institutes of Health, Bethesda, MD

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