molecular-dynamics-guide - Molecular Dynamics Simulation Guide
Setup, run, and analyze molecular dynamics simulations
Tags
Updated: 2026-03-25molecular dynamicssimulationGROMACSOpenMMforce fieldtrajectory analysisfree energybiomolecularcomputational chemistry
Typical Inputs
Typical Outputs
What this skill does
- prepare structure
- assign force field
- solvate system
- add ions
- minimize energy
- equilibrate system
- run simulation
- analyze trajectory
- calculate RMSD
- calculate RMSF
- compute radius of gyration
- analyze hydrogen bonds
- perform umbrella sampling
- compute free energy
Inputs
- PDB structure file
- force field parameters
- ionic strength
- temperature
- pressure
- reaction coordinate
- lambda schedule
Outputs
- simulation trajectory file
- RMSD values
- RMSF values
- radius of gyration data
- hydrogen bond statistics
- free energy profile
Requirements
- GROMACS or OpenMM
- MDAnalysis library
- Python environment
- GPU support
- high performance computing