This repository shows my learning progress and some practice of thermodynamic integration (TI) in AMBER20.
This repository consists of three parts:
- Some basic files and modules of AMBER: antechamber tleap, pmemd, cpptraj.
- Basic molecular dynamics simulation protocol based on AMBER: the protein-ligand complex in water.
- Thermodynamic integration (TI) protocol in AMBER: the calculation of binding energy of the complex.