From: Gumbart, JC (gumbart_at_physics.gatech.edu)
Date: Mon Apr 12 2021 - 07:01:08 CDT
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.
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Dr. Axel Kohlmeyer akohlmey_at_gmail.com<mailto:akohlmey_at_gmail.com> 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!vUkIugtBr4wiDY787KF_QZm1nApBk90ujXA_kvmhMb5RSs0sXXpuIaLWOdKXL4lKGQ$ <https://urldefense.com/v3/__https://pubmed.ncbi.nlm.nih.gov/31265271/__;!!DZ3fjg!u8OlYz6NSYuOtTS1YGhu2-uD3HiVYubDh85Fof-mYvFDUzvIZv2MoYO_68s6tKby0g$> and the supplemental files for examples.
Best,
JC
On Dec 3, 2020, at 10:35 PM, Mohammed umar Sheriff <ms7.umar185_at_gmail.com<mailto:ms7.umar185_at_gmail.com>> wrote:
Ask the suitable person whose details are visible in the webpage namd-l: Re: Hydrogen Mass Repartitioning in NAMD (uiuc.edu)<https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2018-2019/0248.html>
Sent from Mail<https://urldefense.com/v3/__https://go.microsoft.com/fwlink/?LinkId=550986__;!!DZ3fjg!u8OlYz6NSYuOtTS1YGhu2-uD3HiVYubDh85Fof-mYvFDUzvIZv2MoYO_68sUWWfI0A$> 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
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Dipl.-Phys. René Hafner
TU Kaiserslautern
Germany
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