Here is a comparative table highlighting the key differences between NAMD and CHARMm in classical molecular dynamics simulations, covering aspects such as functionality, computational efficiency, system size, and use cases: FeatureNAMDCHARMm Primary FunctionSpecialized in parallel molecular dynamics simulations for large systems.Molecular dynamics simulation software focused on force field calculations. DeveloperDeveloped by the Theoretical and Computational Biophysics Group (TCBG).Developed by Accelrys/BIOVIA. Computational EfficiencyHighly optimized for parallel processing on clusters and supercomputers.Efficient for smaller systems; less focus on large-scale parallelization. Force Fields SupportedPrimarily uses CHARMM force fields but supports AMBER (biomolecular simulation program) and others.Based on the CHARMM (Chemistry at Harvard Molecular Mechanics) force field. System SizeSuitable for large biomolecular systems, such as proteins and membranes.Ideal for smaller systems and QM/MM simulations. GPU SupportExtensive GPU support for acceleration using CUDA.Limited GPU acceleration via DOMDEC and OpenMM. Advanced FeaturesSupports advanced simulations like steered MD, replica exchange MD.Strong support for QM/MM simulations and ligand docking. Use CasesBest for large-scale, high-performance simulations of proteins and membranes.Used for drug design, ligand docking, and detailed force field analysis. Ease of UseRequires some setup complexity for parallel computing.Easier to set up for smaller systems or when integrated into Discovery Studio. Community SupportWidely used in academic research with large user community.More niche, used often in industry for drug discovery.