AW: Hydrogen Mass Repartitioning

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Dec 04 2020 - 03:00:59 CST

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] Im Auftrag
von Gumbart, JC
Gesendet: Freitag, 4. Dezember 2020 04:57
An: namd-l_at_ks.uiuc.edu; Mohammed umar Sheriff <ms7.umar185_at_gmail.com>
Cc: McGuire, Kelly <mcg05004_at_byui.edu>
Betreff: Re: namd-l: Hydrogen Mass Repartitioning

 

Also, have a look at https://pubmed.ncbi.nlm.nih.gov/31265271/ 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.ht
ml>

 

Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> 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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