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Finn Beruldsen

@finnberuldsen.bsky.social

Finn Beruldsen @finnberuldsen.bsky.social · 17/03/2026

(4/4) Open source and ready to test: 📄 www.nature.com/articles/s41... 💻 github.com/AntunesLab/r... 🎥 youtu.be/UoN0GQKHCsw Co-authors: @dinler.bsky.social @martiela.bsky.social . VMD help: @rcbernardi.bsky.social , Diego Gomes. @gromacs.bsky.social #MolecularDynamics #RMSD #RMSF #CompChem #VMD 🧬🖥️

github.com

GitHub - AntunesLab/rmsx: RMSX and Flipbook Package: Time series RMSF combing the features of RMSD and RMSF

RMSX and Flipbook Package: Time series RMSF combing the features of RMSD and RMSF - AntunesLab/rmsx

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Finn Beruldsen @finnberuldsen.bsky.social · 17/03/2026

(3/4) We paired this with Flipbook, which maps those per-residue metrics directly onto structural snapshots in VMD. It helps isolate specific dynamic shifts, like analyzing complex binding interfaces or cross-reactivity. It’s compatible with NAMD, GROMACS, AMBER, and OpenMM.

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Finn Beruldsen @finnberuldsen.bsky.social · 17/03/2026

(2/4) Typically, RMSD shows global structural changes, and RMSF averages out those fluctuations over time. In the GIF, you can see how we try to bridge this gap. RMSX provides a time-resolved view of residue motion, letting you see the evolution of the structure.

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Finn Beruldsen @finnberuldsen.bsky.social · 17/03/2026

(1/4) I'm a 4th year Biochemistry PhD student and I made a tool to help researchers see when and where proteins move. MD generates a lot of data, but connecting where motion occurs with when it happens is surprisingly difficult. RMSX and Flipbook highlight both clearly. 🧵👇

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Reposted by Finn Beruldsen

Dinler Antunes @dinler.bsky.social · 12/03/2026

Ever seen an RMSD spike in a molecular dynamics simulation and wondered: What actually moved? Which residues? Our new @springernature.com paper introduces RMSX + Flipbook for time-resolved MD trajectory analysis 👇 #MolecularDynamics #ComputationalChemistry #ScientificPython #OpenScience

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