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molecular-dynamics-guide
Molecular dynamics simulation setup, execution, and trajectory analysis
skills/domains/chemistry/molecular-dynamics-guide/SKILL.md
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# Molecular Dynamics Guide
A skill for setting up, running, and analyzing molecular dynamics (MD) simulations. Covers force field selection, system preparation, simulation protocols, trajectory analysis, and free energy calculations using GROMACS, OpenMM, and MDAnalysis.
## System Preparation
### Building a Simulation System
The standard workflow for preparing an MD simulation:
```
1. Obtain structure (PDB, homology model, or docking pose)
2. Clean structure (add missing atoms, fix protonation states)
3. Assign force field parameters