NAMD

  • Level of openness 3 ★★★
  • Document quality 3 ★★★

An open-source application for molecular dynamics simulation of biomolecules, especially designed for massively parallel computing. This package enables us to perform efficient parallel calculation on parallel computers ranging from 100 to 20,000 cores. For preparation of calculation and analysis of orbits, it uses visualization software VMD. It supports file formats compatible with other applications such as AMBER and CHARMM, and can be used on various computing environments.

To Detail

myPresto

  • Level of openness 3 ★★★
  • Document quality 3 ★★★

Commercially-available free software for Computer-Aided Drug Development. It includes programs for compound database, protein-compound docking, structure-based drug screening, ligand-based drug screening, protein-ligand binding site prediction, molecular editor, physical property prediction, synthetic accessibility prediction, thermodynamic calculation including multi-canonical dynamics, and molecular dynamics simulations with and without acceleration using GPUs and MPI parallelization.

To Detail

PLUMED

  • Level of openness 3 ★★★
  • Document quality 3 ★★★

An open source library to calculate free energy in molecular dynamics simulation. It supports several famous molecular dynamics software packages such as Amber and Lammps.

To Detail

OVITO

  • Level of openness 3 ★★★
  • Document quality 3 ★★★

An open-source application for visualization of atoms and molecules developed for molecular dynamics. This application supports a number of input file formats for molecular configration, and can perform visualization of three-dimensional atom configration as well as creation of a animation. The main feature of this application is that various useful analysis tools can be used by intuitive control of a graphical user interface (GUI).

To Detail

HOOMD-blue

  • Level of openness 3 ★★★
  • Document quality 3 ★★★

An open-source multi-purpose application for many-particle simulation. This application prepares various kinds of statistical methods and potentials, and can perform simulation of rigid-body mechanics, Langevin dynamics, dissipative-particle dynamics, nonequilibrium molecular dynamics, and so on. It prepares python scripts for production of initial conditions, job submission, and analysis of results.

To Detail

OpenKIM

  • Level of openness 3 ★★★
  • Document quality 3 ★★★

Open-source tools and a database for molecular simulation. Data of molecular models (interatomic potentials and force fields), result data of molecular simulation, and test tools can be downloaded freely. API (Application Programming Interface) for exchanging information between atomistic simulation codes and interatomic models is also provided.

To Detail

LAMMPS

  • Level of openness 3 ★★★
  • Document quality 3 ★★★

A general-purpose open-source application for classical molecular dynamics simulation, distributed under the GPL license. This package can perform molecular dynamics calculation of various systems such as soft matters, solids, and mesoscopic systems. It can be used as a simulator of classical dynamics of realistic atoms as well as general model particles. It supports parallel computing through spatial divisions. Its codes are designed so that their modification and extension are easy.

To Detail

Amber

  • Level of openness 0 ☆☆☆
  • Document quality 3 ★★★

Program package for molecular dynamics simulation. This package includes various material parameters such as peptides, proteins, nuclear acids, carbohydrates, ligands etc., and can perform molecular dynamics simulation of biological macromolecule and cells. This package consists of software for input preparation, simulation, and analysis of results, and is widely used in pharmacy and biological science.

To Detail

PIMD

  • Level of openness 3 ★★★
  • Document quality 3 ★★★

An open-source application for molecular simulations. This application supports various methods such as classical and ab initio molecular dynamics, path integral simulations, replica exchange simulations, metadynamics, string method, surface hopping dynamics, QM/MM simulations, and so on. A hierarchical parallelization between molecular structures (replicas) and force fields (adiabatic potentials) enables fast and efficient computation.

To Detail

J-OCTA

  • Level of openness 0 ☆☆☆
  • Document quality 3 ★★★

A unified application for soft materials simulation. This is a commercial application based on OCTA, and includes modeling/analysis tools for individual simulation engines, use-case databases, tools for structure-property relationship analysis as well as basic functions of OCTA. In particular, VSOP, an original solver for molecular dynamics, is added for fast simulation by MPI parallel computing.

To Detail