From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Jan 31 2020 - 10:35:02 CST
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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