Periodic Boundary Conditions (PBC)

[yutengyan]

I am currently implementing a method to calculate the Lindemann index for my molecular dynamics simulations. However, I have some uncertainties regarding the proper handling of Periodic Boundary Conditions (PBC) when computing atomic distances. Specifically, I'm unsure whether the minimum image convention is being correctly applied in my distance calculations, which is crucial for accurately reflecting atomic vibrations across the simulation box boundaries. Could you provide guidance or best practices on how to effectively incorporate PBC into the Lindemann index calculation to ensure the results are both accurate and reliable?

[github-actions]

Hello @yutengyan, thank you for your interest in our work!

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