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.
PARATEC is a parallel DFT program package based on plane-wave basis and norm-conserving pseudopotential.
Pomerol is an app for calculation one- and two-body Green’s function at finite temperatures for the Hubbard-type model based on the full exact diagonalization. Pomerol is written in C++ and supports the hybrid parallelization (MPI+openMP).
Open source library to record execution and communication time during specified regions in user’s program. C/C++ and Fortran API are provided. This can profile MPI & OpenMP hybrid parallel programs as well as serial ones.
Parsec is a DFT program package based on real space basis and norm-conserving pseudopotential.
PolyParGen is a free web application that automatically generates OPLS force field for molecular dynamics calculations. It is possible to create OPLS-AA parameters of macromolecules such as fullerenes with complex crosslinking structures, graphene and cyclic molecules. The generated OPLS-AA force field parameter file in Gromacs format is automatically sent to users.
Library for calculating Pfaffian (square root of determinant), which is defined for skew-symmetric matrices. Algorithms are implemented in several languages (Fortran, Python, Matlab, Mathematica) and users can choose favorite one. Interfaces for C are also provided.
Python-based simulations of chemistry framework (PySCF) is a general-purpose electronic structure platform written in Python. Users can perform mean-field and post-mean-field methods with standard Gaussian basis functions. This package also provides several interfaces to other software such as BLOCK and Libxc.
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.
An application for three-dimensional visualization with the ray tracing method. This application can visualize arbitrary positions and shapes of objects such as spheres and cubes. It can visualize three-dimensional data obtained from computational fluid dynamics etc. by volume rendering. It can also be used for simple three-dimensional graphical simulator with macro functions.