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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    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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    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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    Parsec

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

    Parsec is a DFT program package based on real space basis and norm-conserving pseudopotential.

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    PFAPACK

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

    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.

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    PySCF

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

    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.

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    PHASE

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

    An electronic structure calculation program based on the density functional theory and the pseudo potential scheme with a plane wave basis set. This is a powerful tool to predict the physical properties of unknown materials and to simulate experimental results such as STM and EELS. This also enables users to perform long time molecular dynamics simulations and to analyze chemical reaction processes. This program is available on a wide variety of computers from single-core PCs to massive parallel computers like K computer. The whole source code is open to public.

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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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