domains / families / science / molecular-dynamics

molecular-dynamics

combined

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. Runs and analyzes molecular dynamics simulations with OpenMM and MDAnalysis. Sets up protein/small molecule systems, defines force fields, runs energy minimization and production MD, and analyzes trajectories (RMSD, RMSF, contact maps, free energy surfaces). For structural biology, drug binding, and biophysics.

When to use

• **Protein stability analysis**: How does a mutation affect protein dynamics?
• **Drug binding simulations**: Characterize binding mode and residence time of a ligand
• **Conformational sampling**: Explore protein flexibility and conformational changes
• **Protein-protein interaction**: Model interface dynamics and binding energetics
• **RMSD/RMSF analysis**: Quantify structural fluctuations from a reference structure
• **Free energy estimation**: Compute binding free energy or conformational free energy
• **Membrane simulations**: Model proteins in lipid bilayers
• **Intrinsically disordered proteins**: Study IDR conformational ensembles

Skill page

Conflict

The two copies describe the same OpenMM/MDAnalysis workflow, but they disagree on environment setup, version pinning, platform selection, and minimization parameters. The K-Dense copy is more rigorous (dedicated venv, pinned versions, explicit platform argument, 2 fs integrator, neutralization flag, and a warning that trajectories alone do not establish binding free energy), while the FreedomIntelligence copy adds a conda/pip install path and a CUDA/OpenCL/CPU fallback. Neither is a strict superset of the other, so crowning one would hide a real alternative.