On Mon, Nov 10, 2025, Wong, Matthew via AMBER wrote:
>
>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?
It's hard to say much based on only 2 ns of simulation and the small amount
of information we have.
A solute restraint of 100 is very high: consider reducing that by an order
of magnitude.
In the NPT simulation, see if the density and volume are changing by a lot;
that could lead to changes in your RMS statistic.
Generally, a single number is not going to tell you all that much. Visual
examination is always recommended.
...good luck...dac
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Received on Mon Nov 10 2025 - 07:30:02 PST
