GROMACS 4.5 is a high-throughput and highly parallel open-source molecular simulation toolkit designed for efficient and scalable simulations of biomolecules. The software supports a wide range of biomolecules, including proteins, nucleic acids, and lipids, and comes with commonly used force fields. New features include implicit solvent models, free-energy algorithms, and multithreading for efficient parallelization on low-end systems. The software also includes hand-tuned assembly kernels and state-of-the-art parallelization techniques, providing high performance and cost efficiency for both high-throughput and massively parallel simulations. GROMACS is available as open-source software and can be used on various platforms, including Windows, Linux, and cloud computing environments. The development of GROMACS has been driven by the need for efficient modeling, with a focus on achieving high simulation efficiency on small to medium-sized clusters. The software has been optimized for single-node parallelization and strong scaling on massively parallel clusters, making it suitable for both small-scale and large-scale simulations. Additionally, GROMACS supports automated topology generation for a wide range of molecules and force fields, and includes a state-of-the-art free-energy calculation toolbox based on Bennett Acceptance Ratios (BAR). The software's performance has been significantly improved through enhancements in long-range electrostatics calculations, such as 2D pencil node decomposition for particle-mesh Ewald (PME) and improved dynamic load-balancing algorithms. GROMACS 4.5 also offers a cost-efficient simulation performance on small systems, making it accessible for high-throughput simulations on individual nodes.GROMACS 4.5 is a high-throughput and highly parallel open-source molecular simulation toolkit designed for efficient and scalable simulations of biomolecules. The software supports a wide range of biomolecules, including proteins, nucleic acids, and lipids, and comes with commonly used force fields. New features include implicit solvent models, free-energy algorithms, and multithreading for efficient parallelization on low-end systems. The software also includes hand-tuned assembly kernels and state-of-the-art parallelization techniques, providing high performance and cost efficiency for both high-throughput and massively parallel simulations. GROMACS is available as open-source software and can be used on various platforms, including Windows, Linux, and cloud computing environments. The development of GROMACS has been driven by the need for efficient modeling, with a focus on achieving high simulation efficiency on small to medium-sized clusters. The software has been optimized for single-node parallelization and strong scaling on massively parallel clusters, making it suitable for both small-scale and large-scale simulations. Additionally, GROMACS supports automated topology generation for a wide range of molecules and force fields, and includes a state-of-the-art free-energy calculation toolbox based on Bennett Acceptance Ratios (BAR). The software's performance has been significantly improved through enhancements in long-range electrostatics calculations, such as 2D pencil node decomposition for particle-mesh Ewald (PME) and improved dynamic load-balancing algorithms. GROMACS 4.5 also offers a cost-efficient simulation performance on small systems, making it accessible for high-throughput simulations on individual nodes.