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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VASPsol

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

Application for performing first-principles simulations with an implicit solvent model. The code is released as a patch to VASP. The user can perform molecular dynamics as well as reaction analysis using e.g., nudged elastic band method.

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RISM/3D-RISM

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

This is a structure analysis program for solutes and solvents, based on the statistical mechanics theory of liquids. The program determines the solvent density distribution surrounding the solute, and calculates various physical values such as the solvation free energy, compressibility, and partial molar volume. The program implements a parallelized fast Fourier transform routine for large-scale parallel computing, and can analyze molecular functions such as the ligand binding affinity of proteins, that would be difficult using other methods.

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RuNNer

  • Level of openness 1 ★☆☆
  • Document quality 2 ★★☆

FORTRAN-based software package developed by the Behler Group for implementing Behler-Parinello neural network potentials. Potentials can be constructed, evaluated, and used for molecular dynamics simulations using LAMMPS. The newest generation of neural network potentials that take into account long-range electrostatic interactions are implemented.

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MLIP

  • Level of openness 1 ★☆☆
  • Document quality 2 ★★☆

Software package that implements moment tensor potentials. Potentials can be trained and used for molecular dynamics calculations using LAMMPS. Active learning combined with molecular dynamics calculations is also available.

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GULP

  • Level of openness 0 ☆☆☆
  • Document quality 2 ★★☆

An application program for lattice dynamics calculation of molecules, surfaces, and solids in various boundary conditions. It lays emphasis on analytic calculation of lattice dynamics while it can perform molecular dynamics simulation as well. It supports various force fields to treat ionic materials, organic materials, and metals. It also implements analytic derivatives of the second and third order for many force fields.

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TINKER

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

An open-source application for molecular dynamics. This application can perform molecular dynamics simulation of biopolymers and solvents consisting of a number of molecules/atoms. It implements a number of force field sets and algorithms, and supports parallel computing based on OpenMP. Java graphical user interface (GUI) is also included.

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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.

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CHARMM

  • Level of openness 0 ☆☆☆
  • Document quality 2 ★★☆

A general-purpose application for molecular dynamics simulation equipped with many tools. This package was originally developed for biomolecules (peptides, proteins, nuclear acids, etc.), and the current version can perform molecular dynamics simulation for various systems such as solutions, crystals, membranes, and so on. It supports several sampling methods and calculation of free energy. It also supports various computing environments including both serial and parallel computers.

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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.

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