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 Sun Nov 09 2025 - 22:00:02 PST
