Molecular dynamics (MD) simulations have become an essential tool for studying the dynamics of biological systems and exploring protein-ligand interactions. is a modern, open-source software toolkit designed for MD simulations. Until now, it has lacked a module dedicated to building receptor-ligand systems, which is highly useful for investigating protein-ligand interactions for drug discovery. We therefore introduce , an open-source toolkit that enables the preparation and simulation of protein-ligand complexes in , along with the subsequent analysis of protein-ligand interactions. consists of three main components: , a graphical user interface based on Python to prepare protein and simulation settings, to perform MD simulations with consecutive trajectory postprocessing, and finally to analyze simulation results with respect to ligand binding. is not only a versatile tool for analyzing protein-ligand interactions and generating ligand binding modes throughout simulations; it also tracks and clusters water molecules, particularly those exhibiting minimal displacement from their previous coordinates, providing insights into solvent dynamics. We applied to study ligand-receptor interactions across diverse biological systems, including LDN-193189 and LDN-212854 with ALK2 (kinases), nifedipine and amlodipine in Ca1.1 (ion channels), LSD in 5-HT (G-protein coupled receptors), letrozole in CYP19A1 (cytochrome P450 oxygenases), flavin mononucleotide binding the FMN-riboswitch (RNAs), ligand C08 bound to TLR8 (toll-like receptor), and PZM21 bound to MOR (opioid receptor), highlighting distinct functionalities of . is publicly available at https://github.com/wolberlab/OpenMMDL.