Typo... 4fs and dt=0.004
_____________________
Zhen Li<
http://lizhen62017.wixsite.com/home>, Ph.D.,
The Merz Research Group<
http://merzgroup.org/>,
Michigan State University,
Cleveland Clinic.
________________________________
From: Li, Zhen via AMBER <amber.ambermd.org>
Sent: Wednesday, April 15, 2026 1:41 PM
To: AMBER Mailing List <amber.ambermd.org>; saverio lemme <saverio.lemme.alumni.uniroma2.eu>
Subject: Re: [AMBER] R: Question regarding the relaxation of a system and the use of HMR
Hi Saverio,
I agree with what Dr. Giese and Dr. Roitberg said: a long equilibration is unnecessary. A short simulation after HMR is more than enough, especially when you set the 4 ns simulation step, "dt=0.04", as tutorial 13 mentions.
Best regards,
Zhen.
_____________________
Zhen Li<
https://urldefense.com/v3/__http://lizhen62017.wixsite.com/home__;!!HXCxUKc!2X4J1SDR-3u1HJzON_PBgoXYFpDRydFpXHiiwGT4AwL5raVHvkWHt2JrHzHSAjTDq1zaghEoAjl3byynucKKB14$ >, Ph.D.,
The Merz Research Group<
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Michigan State University,
Cleveland Clinic.
________________________________
From: saverio lemme via AMBER <amber.ambermd.org>
Sent: Wednesday, April 15, 2026 10:33 AM
To: Adrian Roitberg <roitberg.ufl.edu>; AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] R: Question regarding the relaxation of a system and the use of HMR
Ok.
Thanks.
Saverio
________________________________
Da: Adrian Roitberg via AMBER <amber.ambermd.org>
Inviato: mercoledì 15 aprile 2026 15:30
A: saverio lemme via AMBER <amber.ambermd.org>
Oggetto: Re: [AMBER] Question regarding the relaxation of a system and the use of HMR
Hi Severio
Interesting question. I do not think a new equilibration is strictly
needed, but I would do a short one anyways
Adrian
On 4/15/26 6:04 AM, saverio lemme via AMBER wrote:
> [External Email]
>
> Hi,
> I prepared a complex of two proteins, performed the relaxation
> of explicit water system according to tutorial 13, and then applied
> HMR according to tutorial 12.
> Since a change was made to the masses of some atoms, is a
> new relaxation step necessary?
> If so, is there a tutorial or suggestions for performing it?
> Probably a relaxation with fewer steps?
>
> Thanks.
>
> Saverio Lemme
>
>
>
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Department of Chemistry
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roitberg.ufl.edu
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Received on Wed Apr 15 2026 - 11:00:03 PDT
