For the sake of completeness, while it is true that the potential energy
does NOT depend on mass, the kinetic energy does. HMR is design not to
change the overall kinetic energy, but it will affect things locally
(i.e. the velocities of the methyl group with and without HMR will be
slightly different.)
That is why I recommended a short equilibration. Not because of the
structure, but to make sure the local velocities have time to adjust.
That should happen VERY fast, in the tens of ps regime.
Adrian
On 4/15/26 1:45 PM, Li, Zhen via AMBER wrote:
> [External Email]
>
> 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<http://lizhen62017.wixsite.com/home >, Ph.D.,
>
> The Merz Research Group<http://merzgroup.org/ >,
>
> 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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>> http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber%7C02%7Csaverio.lemme%40alumni.uniroma2.eu%7C9ae2672d4e15422844a008de9af3ad24%7C24c5be2ad76440c5997582d08ae47d0e%7C0%7C0%7C639118568563730783%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=rAwHFLJLOfg8Ej1PTjUm5oze128U2AyAYXfsljouSpU%3D&reserved=0 <http://lists.ambermd.org/mailman/listinfo/amber >
> --
> Dr. Adrian E. Roitberg
> Frank E. Harris Professor
> Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
>
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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 - 11:30:02 PDT
