drug-protein-ligand-md

Goal

To run a complete protein-ligand molecular dynamics simulation using OpenMM, starting from a system bundle produced by drug-complex-system-builder. The workflow includes:

1. Energy minimization
2. NVT equilibration with positional restraints on heavy atoms
3. NPT equilibration with restraints gradually released
4. NPT production run

The output is a DCD trajectory + final state checkpoint suitable for drug-trajectory-analysis.

Instructions

1. Prepare inputs

Required from drug-complex-system-builder:

• system.xml: serialized OpenMM System
• complex_solvated.pdb: solvated complex PDB (used as topology reference)