A structure database for proteins and nuclear acids. Three-dimensional structure data of proteins and nuclear acids (atomic coordinates determined experimentally by X-ray crystal analysis, NMR, etc.) can be downloaded. The data reposited in PDB are in the public domain, and can be accessed by everyone freely.
xTAPP is a first-principles plane-wave pseudo-potential code. It computes band structure and electronic states with high precision for a wide range of materials including metals, oxide surfaces, solid interfaces, and so forth. It has support tools and visualization of output and input, is available as a massively parallel computer using OpenMP, MPI, and GPGPU.
An application for adding a function of the replica exchange method to the existing applications for molecular dynamics simulation such as MODYLAS, AMBER, and CHARMM. Without changing original programs of molecular dynamics, the replica exchange method can be implemented easily. This application also shows high performance in massive parallel computing by the K-computer.
An open-access database of crystal structures. This database includes structural data of organic, inorganic, metal-organic compounds and minerals. At the end of 2017, this database contains about 400,000 entries. Three-dimensional structures of crystals can be viewed by GUI on the web.
Provides a complete set of environments necessary for computational materials science research in the cloud. A web browser is all that is needed to start a full range of first-principles simulations, including modeling, calculation, data storage, and analysis. RSDFT is used as the engine, and the lineup will be expanded in the future. Data can be shared within a group, and structural data from other software such as GAUSSIAN and VASP can be read.
DDMRG (DynamicalDMRG) is a program for analyzing the dynamical properties of one-dimensional electron systems by using the density matrix renormalization group method. It simulates excited or photo-induced quantum phenomena in Mott insulators, spin-Peierls materials, organic materials, etc. Parallel computational procedures for linear and non-linear responses in low dimensional electron systems and analyzing routines for relaxation processes of excited states induced by photo-irradiation are available.
This software is for constructing inter-atomic force fields that mostly fit the results of ab-initio calculations, using multi-canonical molecular dynamic simulations. Various potential functions such as silicon, ionic crystal, and water have been pre-installed, and the user’s potential function can also be used. The default ab initio calculation solver is xTAPP and other calculation libraries are also applicable.
An open-source application for electronic structure calculation based on the diffusion Monte Carlo method. By using output of other packages of first-principles quantum-chemical calculation, this package performs electronic structure calculation with high accuracy. Although its computational cost is high, various physical quantities can be evaluated very accurately. It implements an efficient parallelization algorithm, and supports massively parallel computing.
An application for structure prediction based on the evolutionary algorithm. From an input of the atomic position in a unit cell and possible elements at each atomic position, this application predicts the stable structure and composition from the first-principles calculation and molecular dynamics in combination with the evolutionary algorithm. This application is written in Python, and uses Quantum ESPRESSO and GULP as an external program.
A GUI program for structure modeling of giant molecules. This application consists of two programs, “fumodel” and “fuplot”. The former supports preparation of input data for FMO in GAMESS, whereas the latter is software for making graphs from numerical results obtained by FMO.