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” ©
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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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