RE: Hydrogen Mass Repartitioning

From: James Kress (jimkress_58_at_kressworks.org)
Date: Sat Dec 05 2020 - 15:43:49 CST

Hello Rafael,

 

Thank you very much for your reply. It is quite useful.

 

Jim

 

James Kress Ph.D., President

The KressWorks® Institute

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

“Engineering The Cure” ©

(248) 573-5499

 

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From: Rafael Bernardi <rcbernardi_at_auburn.edu>
Sent: Saturday, December 05, 2020 3:28 PM
To: namd-l_at_ks.uiuc.edu; James Kress <jimkress_58_at_kressworks.org>
Cc: 'Norman Geist' <norman.geist_at_uni-greifswald.de>
Subject: Re: namd-l: Hydrogen Mass Repartitioning

 

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.

 

Best

 

Rafael

 

 

……………………………………………………………………...

Rafael C. Bernardi

Biophysics Cluster - Department of Physics at Auburn University

NIH Center for Macromolecular Modeling & Bioinformatics

 <mailto:rcbernardi_at_auburn.edu> rcbernardi_at_auburn.edu

 <mailto:rcbernardi_at_ks.uiuc.edu> rcbernardi_at_ks.uiuc.edu

 <http://www.ks.uiuc.edu/~rcbernardi> www.ks.uiuc.edu/~rcbernardi

+1 (334) 844-4393

 

 

 

 

 

From: <owner-namd-l_at_ks.uiuc.edu <mailto:owner-namd-l_at_ks.uiuc.edu> > on behalf of James Kress <jimkress_58_at_kressworks.org <mailto:jimkress_58_at_kressworks.org> >
Organization: The KressWorks Foundation
Reply-To: "namd-l_at_ks.uiuc.edu <mailto:namd-l_at_ks.uiuc.edu> " <namd-l_at_ks.uiuc.edu <mailto:namd-l_at_ks.uiuc.edu> >, James Kress <jimkress_58_at_kressworks.org <mailto:jimkress_58_at_kressworks.org> >
Date: Friday, December 4, 2020 at 6:07 PM
To: "namd-l_at_ks.uiuc.edu <mailto:namd-l_at_ks.uiuc.edu> " <namd-l_at_ks.uiuc.edu <mailto:namd-l_at_ks.uiuc.edu> >
Cc: 'Norman Geist' <norman.geist_at_uni-greifswald.de <mailto:norman.geist_at_uni-greifswald.de> >
Subject: RE: namd-l: Hydrogen Mass Repartitioning

 

Can this be done for QM/MM?

 

Jim

 

James Kress Ph.D., President

The KressWorks® Institute

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

“Engineering The Cure” ©

(248) 573-5499

 

Learn More and Donate At:

Website: <http://www.kressworks.org/> http://www.kressworks.org

 

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: owner-namd-l_at_ks.uiuc.edu <mailto:owner-namd-l_at_ks.uiuc.edu> <owner-namd-l_at_ks.uiuc.edu <mailto: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 <mailto:namd-l_at_ks.uiuc.edu> ; 'Gumbart, JC' <gumbart_at_physics.gatech.edu <mailto: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.gov_31265271_&d=DwMFAg&c=OCIEmEwdEq_aNlsP4fF3gFqSN-E3mlr2t9JcDdfOZag&r=jUfnSyKkfkyVRBIUzlG1GSGGZAZGcznwr8YliSSCjPc&m=YnZSRlTzHB_mHnKrQ-Heu4gS2N5ngTIIbFjjjABXK6U&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.html>

 

Sent from Mail <https://urldefense.proofpoint.com/v2/url?u=https-3A__go.microsoft.com_fwlink_-3FLinkId-3D550986&d=DwMFAg&c=OCIEmEwdEq_aNlsP4fF3gFqSN-E3mlr2t9JcDdfOZag&r=jUfnSyKkfkyVRBIUzlG1GSGGZAZGcznwr8YliSSCjPc&m=YnZSRlTzHB_mHnKrQ-Heu4gS2N5ngTIIbFjjjABXK6U&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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