[AMBER] 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 10:04:53 +0000

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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Received on Wed Apr 15 2026 - 03:30:02 PDT