From: René Hafner TUK (hamburge_at_physik.uni-kl.de)
Date: Mon Apr 12 2021 - 07:37:38 CDT
I see, now to slow down the rotation of hydrogen atoms about heavy bond
partners, they need to be made havier.
Got it, thanks a lot to both of you!
On 4/12/2021 2:01 PM, Gumbart, JC wrote:
> Indeed - see this paper, particularly Table 1:
>
> Feenstra KA; Hess B; Berendsen HJC Improving efficiency of large
> time-scale molecular dynamics simulations of hydrogen-rich
> systems. J. Comput. Chem 1999, 20, 786–798.
>
> Best,
> JC
>
>> On Apr 12, 2021, at 7:52 AM, Axel Kohlmeyer <akohlmey_at_gmail.com
>> <mailto:akohlmey_at_gmail.com>> wrote:
>>
>> While keeping bonds with hydrogen atoms rigid, eliminates the need to
>> represent the high frequency motions of those bonds, it does not slow
>> down the rotation of the hydrogen atoms around their heavier bond
>> partners.
>>
>> Axel.
>> --
>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com <mailto:akohlmey_at_gmail.com>
>> https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!vnvupqEoTR2qTp7hmP3ir2pLfJNKYFvbkGXUqHeW-3GSeIQRe9Udvv-BGYtCugxmpg$
>> <https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!vUkIugtBr4wiDY787KF_QZm1nApBk90ujXA_kvmhMb5RSs0sXXpuIaLWOdICQANsWA$>
>> College of Science & Technology, Temple University, Philadelphia PA, USA
>> International Centre for Theoretical Physics, Trieste, Italy
>>
>> On Mon, Apr 12, 2021, 06:35 René Hafner TUK
>> <hamburge_at_physik.uni-kl.de <mailto:hamburge_at_physik.uni-kl.de>> wrote:
>>
>> Dear Mr. Gumbart,
>>
>> why is it that with HMR we increase/repartition the mass
>> of/to hydrogens but then keeping all of them fixed using
>> rigidBonds (according to example NAMD configfile in SI of your
>> paper mentioned below)?
>>
>> Couldn't we have increase ts to 4fs in the first place when
>> we keep all hydrogens fixed anyway?
>>
>> Kind regards
>>
>> René Hafner
>>
>> On 12/4/2020 4:57 AM, Gumbart, JC wrote:
>>> Also, have a look at https://urldefense.com/v3/__https://pubmed.ncbi.nlm.nih.gov/31265271/__;!!DZ3fjg!vnvupqEoTR2qTp7hmP3ir2pLfJNKYFvbkGXUqHeW-3GSeIQRe9Udvv-BGYv617EZUw$
>>> <https://urldefense.com/v3/__https://pubmed.ncbi.nlm.nih.gov/31265271/__;!!DZ3fjg!u8OlYz6NSYuOtTS1YGhu2-uD3HiVYubDh85Fof-mYvFDUzvIZv2MoYO_68s6tKby0g$>
>>> and the supplemental files for examples.
>>>
>>> Best,
>>> JC
>>>
>>>> On Dec 3, 2020, at 10:35 PM, Mohammed umar Sheriff
>>>> <ms7.umar185_at_gmail.com <mailto:ms7.umar185_at_gmail.com>> wrote:
>>>>
>>>> Ask the suitable person whose details are visible in the
>>>> webpagenamd-l: Re: Hydrogen Mass Repartitioning in NAMD
>>>> (uiuc.edu)
>>>> <https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2018-2019/0248.html>
>>>> Sent fromMail
>>>> <https://urldefense.com/v3/__https://go.microsoft.com/fwlink/?LinkId=550986__;!!DZ3fjg!u8OlYz6NSYuOtTS1YGhu2-uD3HiVYubDh85Fof-mYvFDUzvIZv2MoYO_68sUWWfI0A$>for
>>>> Windows 10
>>>> *From:*McGuire, Kelly <mailto:mcg05004_at_byui.edu>
>>>> *Sent:*04 December 2020 08:38
>>>> *To:*namd-l_at_ks.uiuc.edu <mailto:namd-l_at_ks.uiuc.edu>
>>>> *Subject:*namd-l: Hydrogen Mass Repartitioning
>>>> Does anyone have a tutorial on how to implement hydrogen mass
>>>> repartitioning in NAMD? I have never used this method before.
>>>> Thanks!
>>>>
>>>> /Dr. Kelly L. McGuire/
>>>>
>>>> /PhD Biophysics/
>>>>
>>>> /Department of Physiology and Developmental Biology/
>>>>
>>>> /Brigham Young University/
>>>>
>>>> /LSB 3050/
>>>>
>>>> /Provo, UT 84602/
>>>>
>>>
>> --
>> --
>> Dipl.-Phys. René Hafner
>> TU Kaiserslautern
>> Germany
>>
>
-- -- Dipl.-Phys. René Hafner TU Kaiserslautern Germany
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