ESPResSo
ESPResSo, the Extensible Simulation Package for Research on Soft Matter, is a highly versatile open source simulation package for performing and analyzing scientific molecular dynamics and Monte Carlo many-particle simulations. It is designed as a universal tool for simulating a variety of soft matter systems, especially coarse-grained atomistic or bead-spring models used in physics, chemistry, molecular biology, and process engineering. ESPResSo can be used to simulate polymers, liquid crystals, colloids, polyelectrolytes, ferrofluids, gels, biological systems, DNA, lipid membranes, bacterial motion, and super-capacitors. In coarse-grained models, a group of atoms or molecules is treated as a single bead, allowing researchers to investigate larger time and length scales than would be practical with fully atomistic simulations. ESPResSo supports classical molecular dynamics simulations in different statistical ensembles.
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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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Ascalaph Designer
Ascalaph Designer is a general-purpose program for molecular dynamic simulations. Under a single graphical environment are represented as their own implementation of molecular dynamics as well as the methods of classical and quantum mechanics of popular programs. Molecular geometry optimization with conjugate gradient methods. Shows molecular models in separate windows. Each window has two cameras, which allow the model to be simultaneously visualized from two sides and in different graphic modes. The subwindow can be opened by dragging the splitter in the right corner of each graphical window. Clicking on an atom or bond with the left mouse button slightly changes their color and a brief info about the picked object appears in the status bar. The wire-frame style is convenient for large molecules, particularly, proteins. Drawing is very fast for this style. Finally, CPK wire frame combines the properties of several above styles.
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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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