We have prepared protein-ligand complex using outputs of Autodock Vina and later PyMol [19] is used to save as PDB file. To fix missing hydrogen or residues of this complex, we used Swiss PDB Viewer . CHARMM force field was added on ligand using swissparam.ch website . For GROMACS commands, you can visit my GitHub link (). For our ligand-protein complex of 851 amino acids, for 20ns MD simulation, on 2 GPU, 22 GB RAM, NVIDIA 1080 Ti, it took 26 hour time (more than 1 day).