molecular-dynamics-guide - Setup and analyze molecular dynamics simulations
Set up, run, and analyze molecular dynamics simulations using GROMACS and OpenMM
Tags
Updated: 2026-03-25Capabilities
Typical Inputs
Typical Outputs
What this skill does
- prepare simulation system
- process PDB structure
- generate topology
- solvate system
- add counterions
- minimize energy
- equilibrate system
- run production simulation
- assign force field
- analyze trajectory
- calculate RMSD
- calculate RMSF
- compute radius of gyration
- analyze hydrogen bonds
- perform umbrella sampling
- run free energy perturbation
- compute free energy profile
Inputs
- PDB structure
- force field parameters
- trajectory files
- topology files
- simulation parameters
Outputs
- simulation trajectory
- RMSD data
- RMSF data
- hydrogen bond data
- free energy profile
Requirements
- GROMACS
- OpenMM
- MDAnalysis
- Python environment
- GPU support (optional)