# Re: [External Email] 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 - 10:36:51 CST

Dear Giacomo,
Thank you!! I will practice it very soon.
best,
Jiali

On Fri, Jan 31, 2020 at 11:35 AM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:

> It really depends on the system. Why don't you do the exercise I
> suggested, and then extend it to water-ion or ion-ion pairs?
>
> On Fri, Jan 31, 2020 at 11:30 AM Jiali Wang <jwang204_at_binghamton.edu>
> wrote:
>
>> Dear Giacomo,
>> Thank you for your reply and suggestion!
>> 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
>>>>> 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
>>>
>>
>
> --
> 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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