Re: Hydrogen Mass Repartitioning

From: René Hafner TUK (hamburge_at_physik.uni-kl.de)
Date: Mon Apr 12 2021 - 05:33:10 CDT

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

Ren 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!u8OlYz6NSYuOtTS1YGhu2-uD3HiVYubDh85Fof-mYvFDUzvIZv2MoYO_68s6tKby0g$
> <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/
>>
>> /PhDBiophysics/
>>
>> /Department of Physiology and Developmental Biology/
>>
>> /Brigham Young University/
>>
>> /LSB 3050/
>>
>> /Provo, UT 84602/
>>
>

-- 
--
Dipl.-Phys. Ren Hafner
TU Kaiserslautern
Germany

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