molecular-dynamics
K-Dense-AI/scientific-agent-skills
Perform comprehensive molecular dynamics (MD) simulations using high-performance engines like OpenMM and analysis tools like MDAnalysis. This skill allows users to model the time evolution of biological systems, covering system preparation (solvation, force field assignment), energy minimization, NVT equilibration, and advanced analysis (RMSD, free energy surfaces). Ideal for structural biology, drug binding studies, and biophysics research.