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).
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.
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.
An open-source application for analysis and visualization of two- and three-dimensional data. The function of this application can be used not only by interactive operation with three-dimensional display, but also by batch processing. This application supports various environments such as Windows, Mac, and Linux from a desktop PC to a supercomputer performing large scale parallel computation.
An open source library to calculate free energy in molecular dynamics simulation. It supports several famous molecular dynamics software packages such as Amber and Lammps.