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.
Debian Live Linux System that contains OS, editors, materials science application software, visualization tools, etc. An environment needed to perform materials science simulations is provided as a one package. By booting up on VirtualBox virtual machine, one can start simulations, such as the first-principles calculation, molecular dynamics, quantum chemical calculation, lattice model calculation, etc, immediately.
OCTA is an integrated simulation system for soft materials developed by the joint project of industry and academia funded by Ministry of Economy, Trade and Industry(METI), Japan. OCTA consists of four simulation engines named COGNAC(Molecular dynamics simulation), PASTA(rheology simulation), SUSHI(mean field theory), MUFFIN(continuum theory) and a simulation platform (GOURMET).
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.
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.
An open-source multi-purpose application for modeling and visualizing molecules (biomolecules, in particular). This application has been developed for multi-scale molecular simulation, and also provides a simple GUI for AMBER and Gaussian. It also implements exchange of protein residues and the Pathways model for the electron transfer in proteins. It calls rasmol for visualization of atoms and molecules.
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.
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 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.
An open-source application for molecular dynamics simulation of biomolecules, especially designed for massively parallel computing. This package enables us to perform efficient parallel calculation on parallel computers ranging from 100 to 20,000 cores. For preparation of calculation and analysis of orbits, it uses visualization software VMD. It supports file formats compatible with other applications such as AMBER and CHARMM, and can be used on various computing environments.