[AMBER] R: Question regarding the relaxation of a system and the use of HMR

From: saverio lemme via AMBER <amber.ambermd.org>
Date: Wed, 15 Apr 2026 14:33:49 +0000

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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--
Dr. Adrian E. Roitberg
Frank E. Harris Professor
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Wed Apr 15 2026 - 08:00:03 PDT
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