From: Brian Radak (brian.radak_at_gmail.com)
Date: Thu Apr 26 2018 - 09:05:49 CDT
Arguably off-topic:
Is it really well-known that the origin of heavy water effects in this
context is purely classical? 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/
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ncbi.nlm.nih.gov_pmc_articles_PMC2154366_&d=DwMFaQ&c=OCIEmEwdEq_aNlsP4fF3gFqSN-E3mlr2t9JcDdfOZag&r=jUfnSyKkfkyVRBIUzlG1GSGGZAZGcznwr8YliSSCjPc&m=E6ChXudiSEpJP9cog0LnWYe6L4efSrPw6i041LfCT60&s=1q-fj9UL2EjLQySBgH9s4fjcsmC_0K4DjDYE2rwUb9k&e=>
>
> 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
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lmgtfy.com_-3Fq-3Dtip3p-2Bheavy-2Bwater&d=DwMFaQ&c=OCIEmEwdEq_aNlsP4fF3gFqSN-E3mlr2t9JcDdfOZag&r=jUfnSyKkfkyVRBIUzlG1GSGGZAZGcznwr8YliSSCjPc&m=E6ChXudiSEpJP9cog0LnWYe6L4efSrPw6i041LfCT60&s=SAwfM4jr7QH4UDiEuO0-4WV5CFyEc1g5OY7JPR-POyI&e=>
>> >>
>> >> 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://urldefense.proofpoint.com/v2/url?u=http-3A__goo.gl_Q3TBQU&d=DwMFaQ&c=OCIEmEwdEq_aNlsP4fF3gFqSN-E3mlr2t9JcDdfOZag&r=jUfnSyKkfkyVRBIUzlG1GSGGZAZGcznwr8YliSSCjPc&m=E6ChXudiSEpJP9cog0LnWYe6L4efSrPw6i041LfCT60&s=0HtpposKuMJ-oPDi68Mk7C-Fn5MLCnrQSodOp7gz_3I&e=>
>> > https://github.com/giacomofiorin
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_giacomofiorin&d=DwMFaQ&c=OCIEmEwdEq_aNlsP4fF3gFqSN-E3mlr2t9JcDdfOZag&r=jUfnSyKkfkyVRBIUzlG1GSGGZAZGcznwr8YliSSCjPc&m=E6ChXudiSEpJP9cog0LnWYe6L4efSrPw6i041LfCT60&s=36YvIVPj_W2XZAw1A3J6c54KKje0CmrWB0LQPb7CucE&e=>
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__goo.gl_1wk0&d=DwMFaQ&c=OCIEmEwdEq_aNlsP4fF3gFqSN-E3mlr2t9JcDdfOZag&r=jUfnSyKkfkyVRBIUzlG1GSGGZAZGcznwr8YliSSCjPc&m=E6ChXudiSEpJP9cog0LnWYe6L4efSrPw6i041LfCT60&s=8HBtlih22ufwEGt7gVI3fjneEG7ZOBHbn4phIzOauCs&e=>
>> College of Science & Technology, Temple University, Philadelphia PA, USA
>> International Centre for Theoretical Physics, Trieste. Italy.
>>
>
>
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