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

From: Jiali Wang (jwang204_at_binghamton.edu)
Date: Fri Jan 31 2020 - 10:30:02 CST

Dear Giacomo,
I am thinking about a stupid question. So under a regular MD simulation,
How higher the energy barrier a molecular/ ion (Water or Sodium) could
overcome (in a water based environments)? Does it have an energy barrier
number where someposition could never reach? I understand this really
depend on system......
best,
Jiali

On Fri, Jan 31, 2020 at 11:19 AM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:

> 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
>>>
>>> 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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