drug-protein-ligand-md

To run protein-ligand molecular dynamics, this Skill automates the end-to-end OpenMM pipeline: energy minimization, restrained NVT and NPT equilibration, and NPT production, outputting a DCD trajectory and restartable final state.

OpenMM NPT simulation requires a serialized system.xml file and a complex_solvated.pdb structure to drive the phased molecular dynamics protocol and generate trajectory outputs.

Yes, you can run multiple independent replicates of protein-ligand MD simulations with different seeds to assess statistical confidence in pose stability and binding-pocket retention.

Yes, OpenMM molecular dynamics supports checkpoint restart by writing a final_state.xml file and md_provenance.json logs, allowing production DCD trajectories to be resumed.

Automating drug discovery simulations is best handled by chaining minimization, restrained NVT equilibration, restrained-then-released NPT equilibration, and NPT production into a single deterministic phased workflow.

During NPT equilibration in OpenMM, thermodynamic parameters and restraints are configurable to stabilize the solvated complex before releasing restraints for the final production molecular dynamics run.