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.
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.
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.
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.
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.
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.
An application for electronic structure calculations and molecular dynamics simulations based on tight-binding approximation. By the Krylov subspace method, this application performs order-N electronic state calculation for large physical systems including a large number of atoms. It also supports massively-parallel computation using MPI/openMP hybrid parallelism, and has demonstrated calculation of 10^7-atom simulation on the K Computer.
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.
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.
A payware for modeling and visualizing molecules. This software includes a standard editor, ChemDraw, and can perform modeling from chemical structural formula. It implements structure optimization and molecular dynamics by molecular mechanics, and provides useful GUIs for MOPAC, Jaguar, GAMESS, and Gaussian. It can also perform spectroscopy analysis. It is included in high-end packages such as ChemBioOffice and ChemOffice.