NAMD

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.

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.