(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 🧬🖥️

(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.

(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.

(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. 🧵👇

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