ACEMD

ACEMD is a production bio-molecular dynamics (MD) software specially optimized to run on graphics processing units (GPUs) on NVIDIA graphics cards. ACEMD is the world fastest MD engine for a single workstation allowing performance equivalent to over 100 CPUs and microsecond long trajectories. ACEMD reads CHARMM/NAMD and AMBER input files on a simple, yet powerful configuration interface.

AMBER

AMBER allows the ability to use NVIDIA GPUs to accelerate PMEMD for both explicit solvent PME and implicit solvent GB simulations.

Abalone

Abalone is a general purpose molecular modeling program focused on molecular dynamics of biopolymers. In addition, it can interact with external quantum chemical programs NWChem, CP2K and PC GAMESS/Firefly).

CHARMM

CHARMM has been developed with a primary focus on the study of molecules of biological interest, including peptides, proteins, prosthetic groups, small molecule ligands, nucleic acids, lipids, and carbohydrates, as they occur in solution, crystals, and membrane environments

DL-POLY

DL_POLY is a general purpose classical molecular dynamics (MD) simulation software developed at Daresbury Laboratory by I.T. Todorov and W. Smith.

GROMACS

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.

HOOMD-Blue

HOOMD-blue stands for Highly Optimized Object-oriented Many-particle Dynamics -- Blue Edition. It performs general purpose particle dynamics simulations on a single workstation, taking advantage of NVIDIA GPUs to attain a level of performance equivalent to many processor cores on a fast cluster.

LAMMPS

LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.

NAMD

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using gigabit ethernet.

OpenMM

OpenMM is a library which provides tools for modern molecular modeling simulation. As a library it can be hooked into any code, allowing that code to do molecular modeling with minimal extra coding. Moreover, OpenMM has a strong emphasis on hardware acceleration, thus providing not just a consistent API, but much greater performance than what one could get from just about any other code available.