think about these:
- what are the reference coordinates, mask and weight at each step of
relaxation? Are they the same?
- what are the reference coordinates and mask during the rmsd calculation?
are they the same as during the MD steps?
in particular, changing the reference coordinates can lead to jumps.
On Mon, Nov 10, 2025 at 12:41 AM Wong, Matthew via AMBER <amber.ambermd.org>
wrote:
> Hi Amber Community,
>
> I hope you’re doing well. I have a quick question regarding the
> equilibration steps in my simulation.
>
> I am simulating a large system closer to a million atoms. For the heating
> step post minimization (T=100→298 K, 1 ns, constant volume, solute
> restraint = 100) and the subsequent constant pressure equilibration (T=298
> K, 1 ns, solute restraint = 100), I’m observing an RMSD jump of about 1.0
> Å. In contrast, all my other steps typically show RMSD changes around 0.2 Å
> and plateau by the end of the step.
>
> Is it normal to see such a larger RMSD jump switching from NVT to NPT? If
> not, could this indicate an issue with my setup, and what changes do you
> suggest that I can make to my protocol?
>
> Thank you for your guidance!
>
> Best regards,
>
> Matthew
>
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Received on Mon Nov 10 2025 - 08:00:02 PST
