Re: Hydrogen Mass Repartitioning

From: Rafael Bernardi (
Date: Sat Dec 05 2020 - 14:27:45 CST

Hello Jim,

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.



Rafael C. Bernardi
Biophysics Cluster - Department of Physics at Auburn University
NIH Center for Macromolecular Modeling & Bioinformatics<><><>
+1 (334) 844-4393

From: <> on behalf of James Kress <>
Organization: The KressWorks Foundation
Reply-To: "" <>, James Kress <>
Date: Friday, December 4, 2020 at 6:07 PM
To: "" <>
Cc: 'Norman Geist' <>
Subject: RE: namd-l: Hydrogen Mass Repartitioning

Can this be done for QM/MM?


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From: <> On Behalf Of Norman Geist
Sent: Friday, December 04, 2020 4:01 AM
To:; 'Gumbart, JC' <>
Subject: AW: namd-l: Hydrogen Mass Repartitioning

Hey, this isn’t difficult.

In case of Amber files use Parmed and something like

>parm my.prmtop
>outparm my.heave.prmtop

In case of charm you can use the new function of psfgen in VMD:

>package require psfgen
>readpsf my.psf
>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:<> [] Im Auftrag von Gumbart, JC
Gesendet: Freitag, 4. Dezember 2020 04:57
An:<>; Mohammed umar Sheriff <<>>
Cc: McGuire, Kelly <<>>
Betreff: Re: namd-l: Hydrogen Mass Repartitioning

Also, have a look at> and the supplemental files for examples.


On Dec 3, 2020, at 10:35 PM, Mohammed umar Sheriff <<>> wrote:

Ask the suitable person whose details are visible in the webpage namd-l: Re: Hydrogen Mass Repartitioning in NAMD (<>

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From: McGuire, Kelly<>
Sent: 04 December 2020 08:38
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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