MercuryDPM
MercuryDPM is an open source code for discrete particle simulations, designed to simulate the motion of particles or atoms by applying forces and torques from external body forces, such as gravity or magnetic fields, and from particle interaction laws. For granular particles, these forces are typically contact forces, including elastic, plastic, viscous, and frictional interactions, while molecular simulations can use interaction potentials such as Lennard-Jones. MercuryDPM is written as a versatile, object-oriented C++ code and is built to be understandable, flexible, and extensible for researchers and engineers who need to create new simulation models. It is developed extensively for granular applications, while remaining adaptable to other particle-based systems and long-range interactions. Its documentation guides users through installation, running simulations, visualization, analysis, and creating new MercuryDPM codes to model systems of their choice.
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GROMACS
GROMACS is a free and open source suite for high-performance molecular dynamics and output analysis. It is a versatile package for simulating the Newtonian equations of motion for systems with hundreds to millions of particles, with a strong focus on materials modeling, biomolecular simulation, and particle-based systems. GROMACS is primarily designed for biochemical molecules such as proteins, lipids, and nucleic acids, which involve many complicated bonded interactions, but its speed in calculating nonbonded interactions also makes it useful for non-biological systems such as polymers and other materials. It can model ensembles of particles in liquid, solid, or gaseous states and supports a wide range of molecular dynamics workflows, from basic energy minimization and equilibration to production simulations and detailed trajectory analysis.
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LAMMPS
LAMMPS, the Large-scale Atomic/Molecular Massively Parallel Simulator, is a classical molecular dynamics code with a focus on materials modeling. It models ensembles of particles in liquid, solid, or gaseous states and can simulate atomic, polymeric, biological, solid-state, granular, coarse-grained, mesoscopic, or macroscopic systems using many interatomic potentials, force fields, and boundary conditions. LAMMPS can model systems in two or three dimensions, from only a few particles up to billions, and is designed to run efficiently on parallel computers while remaining easy to extend and modify. It includes potentials for solid-state materials such as metals and semiconductors, soft matter such as biomolecules and polymers, and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generally, as a parallel particle simulator at atomic, meso, or continuum scale.
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NAMD
NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, it scales from desktop and laptop computers to high-end parallel platforms, hundreds of cores for typical simulations, and beyond 500,000 cores for the largest simulations. NAMD is built for researchers who need to simulate large molecular systems efficiently while preserving compatibility with widely used molecular modeling workflows. It uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, and it is file-compatible with AMBER, CHARMM, and X-PLOR. It is designed to support biomolecular simulations involving proteins, membranes, nucleic acids, solvents, ions, and other molecular systems where atomic interactions and time-dependent motion need to be studied in detail.
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