AW: Hydrogen Mass Repartitioning

From: Norman Geist (
Date: Fri Dec 04 2020 - 03:00:59 CST

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 (


Sent from Mail <> for Windows


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