An open-source application for molecular simulations. This application supports various methods such as classical and ab initio molecular dynamics, path integral simulations, replica exchange simulations, metadynamics, string method, surface hopping dynamics, QM/MM simulations, and so on. A hierarchical parallelization between molecular structures (replicas) and force fields (adiabatic potentials) enables fast and efficient 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.
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.
An application for adding a function of the replica exchange method to the existing applications for molecular dynamics simulation such as MODYLAS, AMBER, and CHARMM. Without changing original programs of molecular dynamics, the replica exchange method can be implemented easily. This application also shows high performance in massive parallel computing by the K-computer.
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 open-source application for molecular dynamics. This application can perform molecular dynamics simulation of biopolymers and solvents consisting of a number of molecules/atoms. It implements a number of force field sets and algorithms, and supports parallel computing based on OpenMP. Java graphical user interface (GUI) is also included.