MDACP

  • Level of openness 3 ★★★
  • Document quality 2 ★★☆

MDACP (Molecular Dynamics code for Avogadro Challenge Project) is an efficient implementations of classical molecular dynamics (MD) method for the Lennard-Jones particle systems. MDACP Ver. 1.xx adopts flat-MPI and Ver. 2.xx adopts MPI+OpenMP hybrid parallelization.

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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.

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MARBLE

  • Level of openness 3 ★★★
  • Document quality 2 ★★☆

An open-source application for molecular dynamics to simulate biopolymers such as proteins and nuclear acids. This application can perform high-speed molecular dynamics simulation by hybrid parallel computing maintaining high-accuracy energy conservation. This application also support high-speed calculation of long-range interaction based on the particle mesh Ewald method. The code is released under GPL lisense.

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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.

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NWChem

  • Level of openness 3 ★★★
  • Document quality 2 ★★☆

An open-source application for general-purpose quantum chemical calculation, laying emphasis on excited states and time evolution. It is based on time-dependent density functional theory (TDDFT) and the QM/MM calculation. It enables efficient massive parallel computing up to one hundred thousands processes. It supports the relativistic effect and offers the basis choice between the Gaussian basis and the plane-wave basis.

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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.

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MateriApps Installer

  • Level of openness 3 ★★★
  • Document quality 2 ★★☆

A collection of shell scripts for installing open-source applications and tools for computational materials science to macOS, Linux PC, cluster workstations, and major supercomputer systems in Japan. Major applications are preinstalled to the nation-wide joint-use supercomputer system at Institute for Solid State Physics, University of Tokyo by using MateriApps Installer.

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Gromacs

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

Open-source package for molecular dynamics simulation designed for biological macromolecules. This package can perform molecular dynamics simulation of biological macromolecules such as proteins, lipids, and nuclear acids as well as solutions by controlling temperature and pressure. This package can treat long-range interaction and free energy, and is designed for parallel computing.

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ERmod

  • Level of openness 3 ★★★
  • Document quality 2 ★★☆

ERmod is software for calculating the free energy in soft, molecular aggregate. This program rapidly and accurately calculates the free energy of binding of a molecule in the aggregate through combination of the molecular dynamics simulation and the energy-representation theory of solvation. The solubility of a molecule can be determined with ERmod in arbitrary solvent including supercritical fluid and ionic liquid. Assessment is also possible for the binding strength and site of a molecule in micelle, lipid membrane or protein.

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MODYLAS

  • Level of openness 3 ★★★
  • Document quality 1 ★☆☆

MODYLAS is a highly parallelized general-purpose molecular dynamics (MD) simulation program appropriate for very large physical, chemical, and biological systems. It is equipped most standard MD techniques including free energy calculations based on thermodynamic integration method. Long-range forces are evaluated rigorously by the fast multipole method (FMM) without using the fast Fourier transform (FFT) in order to realize excellent scalability. The program enables investigations of large-scale real systems such as viruses, liposomes, assemblies of proteins and micelles, and polymers. It works on ordinary linux machines, too.

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