the scientific simulation, molecular modeling, and data analysis software directory

Tag: Molecular dynamics


FHI-aims, the Fritz Haber Institute ab initio molecular simulations package is an all-electron, full-potential electronic structure code package for computational materials science, capable of modeling isolated molecules and periodic systems (solids, surfaces, etc.). It contains preconstructed hierarchical basis sets across the periodic table and can be used for structure optimization, ab initio molecular dynamics, prediction […]


ACEMD is a molecular dynamics software optimized to run on NVIDIA graphics processing units (GPUs). It can read the popular CHARMM, AMBER, OPLS and Martini force field formats and can be used to simulate proteins, oligosaccharides, nucleic acids, and synthetic polymers. Its most basic version is free. Software Licence: Free and Commercial OS: Linux Rate […]


GROMOS is one of the earliest software packages created in order to simulate bio macromolecules by molecular dynamics methodology. Software Licence: Free and Commercial OS: Windows Rate It:   Recent applications:   Is there a simulation software you know, but you didn’t find it on Suggest one!


YASARA is a molecular-modeling and simulation program with an intuitive user interface powered by PVL (Portable Vector Language), a new development framework that provides enhanced performance. PVL allows to visualize even the largest proteins and enables true interactive real-time simulations with highly accurate force fields on standard PCs, by making use of GPUs. You can […]



LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics code used for simulation of solid-state materials (metals, semiconductors), soft matter (biomolecules, polymers) 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. LAMMPS runs on single […]


SIESTA is both a method and computer program implementation, to perform efficient electronic structure calculations and ab-initio molecular dynamics simulations of molecules and solids. SIESTA’s efficiency stems from the use of strictly localized basis sets and from the implementation of linear-scaling algorithms which can be applied to suitable systems. License: Free Academic License OS: Linux […]


TINKER is designed to be an easily used and flexible system of programs and routines for molecular mechanics and dynamics as well as other energy-based and structural manipulation calculations of larger structures, like biopolymers. It is intended to be modular enough to enable development of new computational methods and efficient enough to meet most production […]

Atomistix ToolKit (ATK)

Atomistix ToolKit (ATK) is a general-purpose atomic-scale modeling platform developed by Quantumwise, which combines a wide range of methods and models, including DFT, semi-empirical models, and classical potentials. It is used to calculate electronic structures, compute transport properties of nanoscale devices using non-equilibrium Green’s function (NEGF) formalism, and perform molecular dynamics calculations. License: Commercial License […]


NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. It scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using gigabit ethernet. License: Commercial and Academic License OS: Linux, Mac, and Windows Rate It:   Is there a simulation software you know, […]

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