From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Jan 31 2020 - 10:18:48 CST
I don't know who is the professor you talked with, but please check your
conversation with him/her and make sure you both understand that small
doesn't mean zero.
As an exercise, why don't you compute a PMF from the g(r) between oxygen
atoms in a box of liquid water?
Giacomo
On Fri, Jan 31, 2020 at 11:15 AM Jiali Wang <jwang204_at_binghamton.edu> wrote:
> 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.
> best,
> Jiali
>
> On Fri, Jan 31, 2020 at 10:22 AM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> wrote:
>
>> 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 <jwang204_at_binghamton.edu>
>> 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
>> http://goo.gl/Q3TBQU
>> https://github.com/giacomofiorin
>>
>
-- 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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