Mm2cML is a web application that structure files can be generated from molecular model images. By carrying out three-dimensional reconstruction using OpenMVG and OpenMVS from molecular model images photographed by smartphones or digital cameras, and arranging atoms on the basis of them, users can obtain structure files (CML format) usable for molecular simulation. The simulation can be carried out on the basis of the structure examined using the molecular model in the real world.
Software package that implements Behler-Parinello type neural network potential. The package provides tools for training and evaluating potentials based on given structure-energy data. It also provides an interface with LAMMPS for performing molecular dynamics calculations.
An open-source application for quantum chemical calculation based on the density-matrix renormalization group (DMRG). For systems with a number of atomic orbitals, low-lying energy eigenvalues can be calculated in high accuracy of order of 1kcal/mol. This application is suitable especially to calculation of multi-orbital systems with one-dimensional topology such as chain-like or circular-like configuration of orbits.
An open-source multi-purpose application for modeling and visualizing molecules (biomolecules, in particular). This application has been developed for multi-scale molecular simulation, and also provides a simple GUI for AMBER and Gaussian. It also implements exchange of protein residues and the Pathways model for the electron transfer in proteins. It calls rasmol for visualization of atoms and molecules.
Payware for first-principles quantum chemical calculation. This application performs molecular orbital calculation based on Hartree-Fock approximation, density functional method, and post-HF methods such as MP, f12, multi-configuration SCF, and coupled cluster method. It also implements calculation by path-integral instanton, quantum Monte Carlo, and density-matrix renormalization group method.
Libtetrabz is a library which perform efficiently the Brillouin-zone integration in the electronic structure calculation in a solid by using the tetrahedron method.
An exact diagonalization package for efficiently solving quantum spin 1/2 lattice models in almost fully spin-polarized sectors. QS3 can treat such systems with quite large system sizes, over 1000 sites. It supports calculations of wavenumber-dependence of energy-dispersion and dynamical spin structure factor.
A tool of input-file preparation and visualization for xTAPP, an application of the first-principle calculation. By graphical user interface (GUI), this application helps xTAPP users for making input files, and visualizes results of wavefunctions, electron densities, and potential profiles into three-dimensional graphics from output files.
An application for prediction of stable and metastable structures from a chemical composition. This application applies particle swarm optimization to predict material structures from results of the first-principles calculation by external packages (VASP, CASTEP, Quantum Espresso, GULP, SIESTA, CP2k). It has been applied to predict not only three-dimensional crystal structures, but also those of clusters and surfaces.
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.