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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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.

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CLUPAN

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

Program libraries for alloy modeling analysis using a cluster expansion method. Energy of alloy systems evaluated by other electronic state calculation libraries is used as an input, and atomic configuration effects are evaluated with the accuracy of a first principles calculation. Ground state structures, evaluation of thermodynamic quantities, equilibrium diagrams, disordering by temperature, etc. can be calculated with high accuracy.

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WIEN2k

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

Program package for first-principles calculation based on all-electron calculation method and augmented plane-wave basis. This package performs electronic-state calculation such as band calculation of solids, structure optimization, first-principles molecular dynamics, and so on. All-electron method, which treats core electrons, improves accuracy in calculation compared with pseudo-potential method, and enables us to obtain chemical shifts related to core electrons. This payware can be used by making a contract with the developer.

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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).

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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.

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USPEX

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

An application for prediction of stable and metastable structures from a chemical composition. For prediction of structures, this application combines the first-principles calculation by external packages (VASP, GULP, siesta, Quantum Espresso, STM4, CP2k, etc.) with various efficient algorithms such as the evolutionary algorithm.
It can be applied to prediction of, e.g., structure of crystals under extreme pressure, nanoparticles, and surface reconstruction.

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Open Babel

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

An open-source application for translating chemical structure format files. More than 110 formats are supported. This application is actively being developed taking into account use and construction of database and application to infomational technology in chemistry (chemoinformatics). A graphical user interface is alsp provided for Windows.

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TensorFlow

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

A numerical library for machine learning. Various functions on machine learning (including supervised learning and unsupervised learning) are implemented in this package. Complex network can be expressed in a simple form by using data flow graphs. Efficient CPU/GPGPU parallel computation is supported to realise efficient operation on large scale data.

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PAICS

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

PAICS is a program of quantum chemical calculation. In this program, fragment molecular orbital (FMO) method is adopted, by which large molecules including biomolecular systems can be treated with several quantum chemical approaches including HF and MP2 methods. At the same time, PaicsView has been developed, which is a supporting program for making input files and analyzing calculation results.

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