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.
Open source software for building and using machine learning potentials based on E(3)-equivariant graph neural networks, which can be trained on output files of simulation codes that can be read by ASE. Molecular dynamics calculations with LAMMPS can be performed using the trained potentials.
Open source software for constructing the Allegro potential model based on E(3)-equivariant graph neural networks and using the potential model for molecular dynamics simulations. The code depends on NequIP and can be run in a similar manner. Allegro scales better than NequIP since it doesn’t rely on message passing and the architecture is strictly local with respect to atom-wise environments.
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.
This is a structure analysis program for solutes and solvents, based on the statistical mechanics theory of liquids. The program determines the solvent density distribution surrounding the solute, and calculates various physical values such as the solvation free energy, compressibility, and partial molar volume. The program implements a parallelized fast Fourier transform routine for large-scale parallel computing, and can analyze molecular functions such as the ligand binding affinity of proteins, that would be difficult using other methods.
An application program for lattice dynamics calculation of molecules, surfaces, and solids in various boundary conditions. It lays emphasis on analytic calculation of lattice dynamics while it can perform molecular dynamics simulation as well. It supports various force fields to treat ionic materials, organic materials, and metals. It also implements analytic derivatives of the second and third order for many force fields.
Application for performing first-principles simulations with an implicit solvent model. The code is released as a patch to VASP. The user can perform molecular dynamics as well as reaction analysis using e.g., nudged elastic band method.
An open-source application for molecular dynamics simulation of biomolecules. This application is optimized for massive parallel computing environments such as the K-computer, and can perform high-speed molecular dynamical simulation of proteins and biomolecules. This application supports both all atoms calculation and coarse-grained model calculation, and can treat extended ensemble such as a replica exchange method. This code is released under GPL license.
An application for structure prediction based on the genetic algorithm. This application can predict the structure and composition of stable phase of crystals, molecules, atomic clusters, and so on by using first-principles calculation and molecular dynamics. This application implements interfaces with various programs such as VASP, LAMMPS, MOPAC, GULP, JDFTx, etc, and runs efficiently on parallel computing architectures.
A general-purpose application for molecular dynamics simulation equipped with many tools. This package was originally developed for biomolecules (peptides, proteins, nuclear acids, etc.), and the current version can perform molecular dynamics simulation for various systems such as solutions, crystals, membranes, and so on. It supports several sampling methods and calculation of free energy. It also supports various computing environments including both serial and parallel computers.