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Biomolecular MD (1 sub-skills: openmm-simulation)
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| name | biomolecular-md |
| description | Biomolecular MD (1 sub-skills: openmm-simulation) |
Biomolecular molecular dynamics simulations using OpenMM for proteins, solvated molecular systems, drug-protein interactions, and soft matter. Covers force field assignment (AMBER, CHARMM, OpenFF), explicit solvent models, free energy calculations, and trajectory analysis with mdtraj.
| Sub-Skill | Directory | Description |
|---|---|---|
| OpenMM Simulation | openmm-simulation/ | Full biomolecular MD workflows: protein-in-water from PDB, small molecule solvation with Open Force Field, temperature annealing, equilibration protocols (NVT/NPT), and trajectory analysis with mdtraj |
What biomolecular simulation do you need?
Protein folding / dynamics / conformational sampling?
--> openmm-simulation/ (Workflow 1: Protein in Water from PDB)
Small molecule solvation free energy / drug-like molecule in water?
--> openmm-simulation/ (Workflow 2: Small Molecule Solvation with OpenFF)
Temperature-driven conformational changes / simulated annealing?
--> openmm-simulation/ (Workflow 3: Temperature Annealing)
Drug-protein binding / ligand-receptor interactions?
--> openmm-simulation/ (Workflow 1 with ligand, or use openmmtools for alchemical FE)
Polymer / soft matter in solution?
--> openmm-simulation/ (Workflow 2 with polymer topology via OpenFF)
Force field selection:
Protein/nucleic acid --> AMBER ff14SB or CHARMM36m
Small organic molecule --> OpenFF (Sage / Parsley) via openff-toolkit
Lipid bilayer --> CHARMM36 lipid parameters
General organic --> GAFF2 (via AmberTools) or OpenFF