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Found 2 Skills
Run and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein/small molecule systems, define force fields, run energy minimization and production MD, analyze trajectories (RMSD, RMSF, contact maps, free energy surfaces). For structural biology, drug binding, and biophysics.
Comprehensive guide for MDAnalysis - the Python library for analyzing molecular dynamics trajectories. Use for trajectory loading, RMSD/RMSF calculations, distance/angle/dihedral analysis, atom selections, hydrogen bonds, solvent accessible surface area, protein structure analysis, membrane analysis, and integration with Biopython. Essential for MD simulation analysis.