The fragment molecular orbital (FMO) method can efficiently do quantum-mechanical calculations of large molecular systems by splitting the whole system into small fragments. The FMO program is distributed within quantum-chemical program suite GAMESS-US. FMO can provide various information regarding the structure and function of biopolymers, such as the interaction between a protein and a ligand.
A support application for preparing input files of molecular dynamics calculation. This application supports manual input of atomic coordinates and bond informations, reading files of protain structure database, and editing data by graphical user interface. It also implements various functions such as addition of hydrogen atoms and composition of data. and can treat a large number of atoms using only a moderate memory cost.
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.
An open-source application for first-principles calculation based on all-electron calculations. In addition to ground-state energy and forces on atoms obtained by density functional theory, it focuses on investigation of excited state properties using time-dependent density functional theory as well as many-body perturbation theory. It is parallelized using MPI and is also optimized for multithreaded math libraries such as BLAS and LAPACK.
An open-source application for first-principles calculation utilizing pseudo-potentials and atom-localized basis sets. This application is capable of performing electronic structure calculations, structural relaxation, and molecular dynamics in a wide range of systems based on density functional theory. By adopting atom-localized basis sets, it realizes high-speed electronic calculation and linear-scaling in suitable computer systems. It can also perform electronic conductance calculations based on non-equilibrium Green’s function method.
Open source software for massively parallel quantum chemistry calculations. Energies and geometries of nano-sized molecules can be calculated without fragmentation. The program supports Hartree-Fock, density functional theory, and second-order Møller-Plesset perturbation theory calculations. The input format, execution method, and program structure are simple, and frequently used routines can be easily extracted.
CONQUEST is a linear-scaling DFT (Density Functional Theory) code based on the density matrix minimization method. Since its computational cost, for both memory and computational costs, is only proportional to the number of atoms N of the target systems, the code can employ structure optimization or molecular dynamics on very large-scale systems, including more than hundreds of thousands of atoms. It also has high parallel efficiency and is suitable for massively parallel calculations.
An open-source application for first-principles molecular dynamics simulation based on pseudo-potential and plane-wave basis set. This application enables accurate molecular dynamics by density functional theory and Car-Parrinello method. It also supports structure optimization, Born-Oppenheimer molecular dynamics, path-integral molecular dynamics, calculation of response functions, the QM/MM method, and excited-state calculation.
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 open-source first-principles calculation library for pseudopotential and all-electron calculations. One of or a mixture of Gaussian and plane wave basis sets can be used. A lot of the development focuses on massively parallel calculations and linear scaling. The user can choose various calculation methods including density functional theory and Hartree-Fock.