From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Apr 26 2018 - 10:04:58 CDT
On Thu, Apr 26, 2018 at 10:05 AM, Brian Radak <brian.radak_at_gmail.com> wrote:
> Arguably off-topic:
>
> Is it really well-known that the origin of heavy water effects in this
> context is purely classical?
as a rule of the thumb: for nuclear quantum effects to matter,
positions have to be highly correlated, e.g. through confinement
and/or low temperature.
otherwise, regular thermal fluctuations and corresponding stochastic
motions will wash them out and temporarily lower barriers where
tunneling might be relevant to the point of it not being relevant.
isotope effects, though, i.e. changes in the dynamics resulting from
doubling or tripling the mass of hydrogen atoms, are quite visible for
water and may justify a reparameterization of classical force field
parameters, considering how much those depend on assuming a mean field
approach for simplifying the interactions.
axel.
> NAMD is not setup to do things like path
> integral MD, which would be needed for proper modeling nuclear quantum
> effects. I've seen recent work in this area (Thomas Markland comes to mind),
> but I recall it being done with a specialized MD engine.
>
> On Thu, Apr 26, 2018 at 9:56 AM, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:
>>
>> Giacomo: I have actually checked the results. The top hit I get is this:
>> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2154366/
>>
>> where the authors develop a modified version of TIP3P they call TIP3P-HW.
>>
>> TL;DR indeed!
>>
>> On 26 April 2018 at 15:50, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>>>
>>> people have done classical MD simulations of heavy water and isotope
>>> effects since more than a decade before i did my first steps in
>>> simulating water, and *that* should already be considered ancient
>>> history by now.
>>>
>>> so this is not exactly a hot new topic anymore and thus not much of a
>>> surprise, that web search results are not popping up straight on top.
>>>
>>> on the other hand, because this is such a well established topic, a
>>> reasonably detailed search of the published literature - which should
>>> be at the beginning of *any* new research project - should have turned
>>> up enough information to answer all the questions that were asked and
>>> thus eliminated the need to post them here.
>>>
>>> axel.
>>>
>>> On Thu, Apr 26, 2018 at 9:35 AM, Giacomo Fiorin
>>> <giacomo.fiorin_at_gmail.com> wrote:
>>> > Have you actually checked the results of the search? The answer is
>>> > there,
>>> > but man, it is so... TL;DR
>>> >
>>> > On Thu, Apr 26, 2018 at 8:20 AM, Jérôme Hénin <jerome.henin_at_ibpc.fr>
>>> > wrote:
>>> >>
>>> >> http://lmgtfy.com/?q=tip3p+heavy+water
>>> >>
>>> >> You're welcome.
>>> >>
>>> >> On 26 April 2018 at 14:02, shyam sharma <shyam14u27_at_gmail.com> wrote:
>>> >>>
>>> >>> Dear all,
>>> >>>
>>> >>> How can I solvate carbon nanotube by heavy water? Can I do this by
>>> >>> simply
>>> >>> changing the mass of hydrogen of normal water? Which water model is
>>> >>> appropriate for this simulation? Can I use the TIP3P water model for
>>> >>> heavy
>>> >>> water?
>>> >>>
>>> >>> Any kind of help will be appreciable.
>>> >>>
>>> >>> Regards
>>> >>> Shyam
>>> >>
>>> >>
>>> >
>>> >
>>> >
>>> > --
>>> > Giacomo Fiorin
>>> > Associate Professor of Research, Temple University, Philadelphia, PA
>>> > Contractor, National Institutes of Health, Bethesda, MD
>>> > http://goo.gl/Q3TBQU
>>> > https://github.com/giacomofiorin
>>>
>>>
>>>
>>> --
>>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>>> College of Science & Technology, Temple University, Philadelphia PA, USA
>>> International Centre for Theoretical Physics, Trieste. Italy.
>>
>>
>
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy.
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2018 - 23:21:02 CST