sk Skill · K-Dense-AI
molecular-dynamics
Run and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein and protein-ligand systems with PDBFixer, choose force fields and water models (AMBER14, CHARMM36m, ff19SB, GAFF2, TIP3P), solvate and add ions, run energy minimization, NVT/NPT equilibration and production MD on GPU, then analyze trajectories for RMSD, RMSF, radius of gyration, hydrogen bonds, native contacts, PCA and free…
Open on skills.sh ↗read 2026-09-17
- installs 8w
- 0
- 30-day movement
- starts with the next reading
- Related entries
- 4
- Connections
- 1
pythonbashPython
- Host repository
- K-Dense-AI/drug-discovery-agent-skills
- Version
- 1.2
- Allowed tools
- Read Write Edit Bash
- Compatible with
- Requires Python 3.11+ with openmm and mdanalysis, best installed from conda-forge, so nanoseconds become days. Trajectory analysis alone runs fine on CPU.
- Licence
- MIT
- Host stars
- 30
- Host language
- Python