Protein Data Bank (PDB)

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.

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PARATEC

  • Level of openness 0 ☆☆☆
  • Document quality 0 ☆☆☆

PARATEC is a parallel DFT program package based on plane-wave basis and norm-conserving pseudopotential.

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PolyParGen

  • Level of openness 0 ☆☆☆
  • Document quality 2 ★★☆

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.

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PyTorch

  • Level of openness 3 ★★★
  • Document quality 3 ★★★

An interface package to use Torch (the open-source numerical library for machine learning) from Python. Users can easily implement deep learning based on neural networks, and can use various state-of-the-art methods. This package supports GPGPU parallel computation, and realises high-speed operation. A front-end interface for C++ is also prepared.

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Phonopy

  • Level of openness 3 ★★★
  • Document quality 3 ★★★

Software to calculate physical quantities related to phonon in solids from result calculated using first principles calculation software. Results calculated from first principles calculation software such as VASP and Wien2k are used as an input.

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psi4

  • Level of openness 3 ★★★
  • Document quality 3 ★★★

An open-source application for quantum chemical calculation. This package implements various methods for quantum chemical calculation such as Hartree-Fock approximation, density functional theory, coupled-cluster method, and CI (configuration interaction) method. The package is written in C++, and provides API for Python, by which users can perform for preparation of setting and execution of calculation.

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PIMD

  • Level of openness 3 ★★★
  • Document quality 3 ★★★

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.

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Pomerol

  • Level of openness 3 ★★★
  • Document quality 1 ★☆☆

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).

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PMlib

  • Level of openness 3 ★★★
  • Document quality 2 ★★☆

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.

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POV-Ray

  • Level of openness 3 ★★★
  • Document quality 3 ★★★

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.

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