Re: Cations spontaneous binding pathway with PMF calculation?

From: Giacomo Fiorin (
Date: Fri Jan 31 2020 - 09:22:02 CST

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.


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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