PARATEC is a parallel DFT program package based on plane-wave 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.
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.
A python library for pre- and post-processing of first-principles electronic structure calculations. As a pre-processing tool, it can automatically generate k-point pathways for first-principles calculations of band structures based on the crystal symmetry. It can also post-process first-principles calculation results to generate band structure and density of states plots with atomic species and orbital contributions, or visualize spin textures and Fermi surfaces. It also provides a functionality for band unfolding.
An application for visualization of biopolymers. This application can visualize biopolymers by using its original command line and graphical user interface, more than 600 settings for visualization, and more than 20 visualization schemes. This application also supports more than 30 file formats such as PDB and multi-SDF, and can utilize sophisticated visualization methods such as the ray tracing.
Software tool for constructing interatomic potentials based on nonlinear atomic cluster expansion. It requires the user to either prepare a fitting dataset based on pandas and ASE, or it can automatically extract data from VASP calculation results. The obtained potentials can be used for molecular dynamics simulations using LAMMPS, and it also provides the capability to calculate extrapolation grades for on-the-fly active learning.
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.
Open Chemistry database that has been in operation since 2004 under the National Institutes of Health (NIH) in the United States. It mainly targets data for small molecules, but information on large molecules such as lipids and peptides are also collected. The database can be accessed via web browser or PUG REST API. The data can be also downloaded from an FTP site.
Parsec is a DFT program package based on real space basis and norm-conserving pseudopotential.