RE: Hydrogen Mass Repartitioning

From: James Kress (
Date: Fri Dec 04 2020 - 17:32:44 CST

Can this be done for QM/MM?




James Kress Ph.D., President

The KressWorksR Institute

An IRS Approved 501 (c)(3) Charitable, Nonprofit Corporation

"Engineering The Cure" C

(248) 573-5499


Learn More and Donate At:

Website: <>


Confidentiality Notice | This e-mail message, including any attachments, is
for the sole use of the intended recipient(s) and may contain confidential
or proprietary information. Any unauthorized review, use, disclosure or
distribution is prohibited. If you are not the intended recipient,
immediately contact the sender by reply e-mail and destroy all copies of the
original message.


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
ABXK6U&s=N2PVAe4SF4sKWCFgR134dw44MGeRTlk1Ak4_ufpk_uA&e=> 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
gTIIbFjjjABXK6U&s=H3eHZcDRrB_jZivYl9SZt0EauMO7yhPu5VjNDF8tyOk&e=> for
Windows 10


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


This archive was generated by hypermail 2.1.6 : Thu Dec 31 2020 - 23:17:14 CST