An open-source application for visualization developed for input and output of GAMESS. This application supports various types of input formats such as GAMESS, XYZ, MolDel, pdb, and CML as well as input by GUI and the Z-matrix format. It can visualize molecular orbitals, electron densities, electrostatic potentials, and normal modes, and can output results into various formats.
Python/C++ based software package that employs deep learning techniques for construction of interatomic potentials. It implements the Deep Potential, which defines atomic environment descriptors with respect to a local reference frame. The output of many first-principles and molecular dynamics applications can be used as training data, and the trained potentials can be used for molecular dynamics calculations using LAMMPS and path integral molecular dynamics calculations using i-PI.
A support application for preparing input files of molecular dynamics calculation. This application supports manual input of atomic coordinates and bond informations, reading files of protain structure database, and editing data by graphical user interface. It also implements various functions such as addition of hydrogen atoms and composition of data. and can treat a large number of atoms using only a moderate memory cost.
CONQUEST is a linear-scaling DFT (Density Functional Theory) code based on the density matrix minimization method. Since its computational cost, for both memory and computational costs, is only proportional to the number of atoms N of the target systems, the code can employ structure optimization or molecular dynamics on very large-scale systems, including more than hundreds of thousands of atoms. It also has high parallel efficiency and is suitable for massively parallel calculations.
A simple open-source application for visualization compatible to Protein Data Bank (PDB) format. This application also supports other formats such as Sybyl, Molden, Mopac, and CHARMM. It is a pioneering piece of software as an interactive PDB viewer.
An open-source application of molecular modeling/editing for quantum chemical calculation. This application supports graphical user interface (GUI) for input-file preparation for software of quantum chemical calculation such as GAMESS, Gaussian, etc., and displays their results by reading output files. It can also make movies in the formats of vector graphics, POV-Ray, and so on.
An open-source application for semi-empirical quantum chemical calculation based on NDDO (neglect of diatomic differential overlap) approximation. This program calculates, for a given molecule or a crystal, molecular orbits and atomic forces, as well as vibration spectra, thermal quantities (heat of formation etc.), isotopic exchange effect, force constant, and so on. It can also treat radicals and ions.
A collection of software tools for molecular dynamics calculations. Various interatomic potentials and tight binding models are implemented, and numerous external applications can be invoked. It also supports training and evaluation of GAP (Gaussian Approximation Potential), which is a form of machine learning potential.
MODYLAS is a highly parallelized general-purpose molecular dynamics (MD) simulation program appropriate for very large physical, chemical, and biological systems. It is equipped most standard MD techniques including free energy calculations based on thermodynamic integration method. Long-range forces are evaluated rigorously by the fast multipole method (FMM) without using the fast Fourier transform (FFT) in order to realize excellent scalability. The program enables investigations of large-scale real systems such as viruses, liposomes, assemblies of proteins and micelles, and polymers. It works on ordinary linux machines, too.
An open-source application for the first-principles calculation based on the all-electron method with localized bases. By adopting the full-potential LMTO method, high-speed electronic state calculation can be performed with a less number of bases compared with the standard all-electron method. There is no restriction on symmetries as in the LMTO-ASA method, and spin polarization and spin-orbit interaction can also be treated.