The universe as balls and springs: molecular dynamics in Python
summary
Shows a working pipeline: setup, run, analyze. Uses OpenMM to run short molecular dynamics (1000 steps ≈ 2×10^−12 s per demo; full runs at ~200 ns), analyzes trajectories with MDAnalysis and visualizes with Plotly. Simulates P‑glycoprotein in membrane with morphine and ATP, and the expected substrate‑flip does not appear — data are under‑sampled. Notes force field limits and new tooling like SMIRNOFF and neural‑network potentials that approach quantum accuracy; scaling and parallel analysis remain the bottleneck.
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chapters (10)
- 0:00Introduction
- 0:38What is PGP
- 6:00MD simulations
- 9:50MD simulations in Python
- 11:19Rootmeansquare deviation
- 16:42Principal component analysis
- 21:44Conclusions
- 25:39Open Force Field
- 27:00Machine Learning
- 28:50Communications
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