From: Rafael Bernardi (rcbernardi_at_auburn.edu)
Date: Sat Dec 05 2020 - 14:27:45 CST
Hello Jim,
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: Fri Dec 31 2021 - 23:17:10 CST
Yes, but saying that it should is another very different question.
If you intend to have a QM/MM simulation where there are no chemical reactions, and where you can leave “rigidbonds all”, I cannot see a problem in using 4fs timestep in a QM/MM simulation (with mass repartitioning). However, if you have no rigid bonds, and you are looking to see a chemical reaction, your timestep should in general be 0.5fs.
Best
Rafael
……………………………………………………………………...
Rafael C. Bernardi
Biophysics Cluster - Department of Physics at Auburn University
NIH Center for Macromolecular Modeling & Bioinformatics
rcbernardi_at_auburn.edu<mailto:rcbernardi_at_auburn.edu>
rcbernardi_at_ks.uiuc.edu<mailto:rcbernardi_at_ks.uiuc.edu>
www.ks.uiuc.edu/~rcbernardi<http://www.ks.uiuc.edu/~rcbernardi>
+1 (334) 844-4393
From: <owner-namd-l_at_ks.uiuc.edu> on behalf of James Kress <jimkress_58_at_kressworks.org>
Organization: The KressWorks Foundation
Reply-To: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>, James Kress <jimkress_58_at_kressworks.org>
Date: Friday, December 4, 2020 at 6:07 PM
To: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>
Cc: 'Norman Geist' <norman.geist_at_uni-greifswald.de>
Subject: RE: namd-l: Hydrogen Mass Repartitioning
Can this be done for QM/MM?
Jim
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From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> On Behalf Of Norman Geist
Sent: Friday, December 04, 2020 4:01 AM
To: namd-l_at_ks.uiuc.edu; 'Gumbart, JC' <gumbart_at_physics.gatech.edu>
Subject: AW: namd-l: Hydrogen Mass Repartitioning
Hey, this isn’t difficult.
In case of Amber files use Parmed and something like
Parmed
>parm my.prmtop
>HMassRepartition
>outparm my.heave.prmtop
In case of charm you can use the new function of psfgen in VMD:
TkConsole
>package require psfgen
>resetpsf
>readpsf my.psf
>hmassrepart
>writepsf my.heavy.psf
In NAMD, you don’t have to change much, simply set:
timestep 4
fullelectfrequency 1
nonbondedfreq 1
and of course use the heavy topology you created.
Have fun!
Norman Geist
Von: owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu> [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Gumbart, JC
Gesendet: Freitag, 4. Dezember 2020 04:57
An: namd-l_at_ks.uiuc.edu<mailto:namd-l_at_ks.uiuc.edu>; Mohammed umar Sheriff <ms7.umar185_at_gmail.com<mailto:ms7.umar185_at_gmail.com>>
Cc: McGuire, Kelly <mcg05004_at_byui.edu<mailto:mcg05004_at_byui.edu>>
Betreff: Re: namd-l: Hydrogen Mass Repartitioning
Also, have a look at https://pubmed.ncbi.nlm.nih.gov/31265271/
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.proofpoint.com/v2/url?u=https-3A__go.microsoft.com_fwlink_-3FLinkId-3D550986&d=DwMFAg&c=OCIEmEwdEq_aNlsP4fF3gFqSN-E3mlr2t9JcDdfOZag&r=jUfnSyKkfkyVRBIUzlG1GSGGZAZGcznwr8YliSSCjPc&m=YnZSRlTzHB_mHnKrQ-Heu4gS2N5ngTIIbFjjjABXK6U&s=H3eHZcDRrB_jZivYl9SZt0EauMO7yhPu5VjNDF8tyOk&e=> 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