RE: Hydrogen Mass Repartitioning

From: James Kress (jimkress_58_at_kressworks.org)
Date: Fri Dec 04 2020 - 17:32:44 CST

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/
<https://urldefense.proofpoint.com/v2/url?u=https-3A__pubmed.ncbi.nlm.nih.go
v_31265271_&d=DwMFAg&c=OCIEmEwdEq_aNlsP4fF3gFqSN-E3mlr2t9JcDdfOZag&r=jUfnSyK
kfkyVRBIUzlG1GSGGZAZGcznwr8YliSSCjPc&m=YnZSRlTzHB_mHnKrQ-Heu4gS2N5ngTIIbFjjj
ABXK6U&s=N2PVAe4SF4sKWCFgR134dw44MGeRTlk1Ak4_ufpk_uA&e=> 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://urldefense.proofpoint.com/v2/url?u=https-3A__go.microsoft.com_fwlin
k_-3FLinkId-3D550986&d=DwMFAg&c=OCIEmEwdEq_aNlsP4fF3gFqSN-E3mlr2t9JcDdfOZag&
r=jUfnSyKkfkyVRBIUzlG1GSGGZAZGcznwr8YliSSCjPc&m=YnZSRlTzHB_mHnKrQ-Heu4gS2N5n
gTIIbFjjjABXK6U&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

 

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