MDACP (Molecular Dynamics code for Avogadro Challenge Project) is an efficient implementations of classical molecular dynamics (MD) method for the Lennard-Jones particle systems. MDACP Ver. 1.xx adopts flat-MPI and Ver. 2.xx adopts MPI+OpenMP hybrid parallelization.
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 open-source application for classical molecular dynamics simulation, distributed under the GPL license. This package can perform molecular dynamics calculation of various systems such as soft matters, solids, and mesoscopic systems. It can be used as a simulator of classical dynamics of realistic atoms as well as general model particles. It supports parallel computing through spatial divisions. Its codes are designed so that their modification and extension are easy.
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.
An open-source application for molecular simulations. This application supports various methods such as classical and ab initio molecular dynamics, path integral simulations, replica exchange simulations, metadynamics, string method, surface hopping dynamics, QM/MM simulations, and so on. A hierarchical parallelization between molecular structures (replicas) and force fields (adiabatic potentials) enables fast and efficient computation.
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.
This is a structure analysis program for solutes and solvents, based on the statistical mechanics theory of liquids. The program determines the solvent density distribution surrounding the solute, and calculates various physical values such as the solvation free energy, compressibility, and partial molar volume. The program implements a parallelized fast Fourier transform routine for large-scale parallel computing, and can analyze molecular functions such as the ligand binding affinity of proteins, that would be difficult using other methods.
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 application program for lattice dynamics calculation of molecules, surfaces, and solids in various boundary conditions. It lays emphasis on analytic calculation of lattice dynamics while it can perform molecular dynamics simulation as well. It supports various force fields to treat ionic materials, organic materials, and metals. It also implements analytic derivatives of the second and third order for many force fields.