i-PI

  • Level of openness 3 ★★★
  • Document quality 2 ★★☆

i-PI is a universal force engine interface written in Python, designed to be used together with an ab-initio (or force-field based) evaluation of the interactions between the atoms. This application includes a large number of sophisticated methods such as replica exchange molecular dynamics (REMD) and path integral molecular dynamics (PIMD). Inter-atomic forces can be computed by using external codes such as CP2K, Quantum ESPRESSO and LAMMPS.

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cdview

  • Level of openness 3 ★★★
  • Document quality 2 ★★☆

An open-source application for visualization of many-particle systems. With simple operation by graphical user interface (GUI) or by command line, this application can visualize particle positions obtained from molecular dynamics simulation as well as three-dimensional scalar quantities such as potential energies. It supports various display options on kinds and shapes of particles, and can also visualize bond formation between particles.

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GISP

  • Level of openness 3 ★★★
  • Document quality 2 ★★☆

An educational support application for molecular dynamics. This application provides a graphical user interface (GUI) for Gromacs. Molecular dynamics simulation of liquid and proteins in solvent can be performed easily by choosing a PDB file on GUI.

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MDACP

  • Level of openness 3 ★★★
  • Document quality 2 ★★☆

MDACP (Molecular Dynamics code for Avogadro Challenge Project) is an efficient implementations of classical molecular dynamics (MD) method for the Lennard-Jones particle systems. MDACP Ver. 1.xx adopts flat-MPI and Ver. 2.xx adopts MPI+OpenMP hybrid parallelization.

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LAMMPS

  • Level of openness 3 ★★★
  • Document quality 3 ★★★

A general-purpose open-source application for classical molecular dynamics simulation, distributed under the GPL license. This package can perform molecular dynamics calculation of various systems such as soft matters, solids, and mesoscopic systems. It can be used as a simulator of classical dynamics of realistic atoms as well as general model particles. It supports parallel computing through spatial divisions. Its codes are designed so that their modification and extension are easy.

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RISM/3D-RISM

  • Level of openness 1 ★☆☆
  • Document quality 1 ★☆☆

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.

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J-OCTA

  • Level of openness 0 ☆☆☆
  • Document quality 3 ★★★

A unified application for soft materials simulation. This is a commercial application based on OCTA, and includes modeling/analysis tools for individual simulation engines, use-case databases, tools for structure-property relationship analysis as well as basic functions of OCTA. In particular, VSOP, an original solver for molecular dynamics, is added for fast simulation by MPI parallel computing.

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TINKER

  • Level of openness 0 ☆☆☆
  • Document quality 0 ☆☆☆

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.

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GULP

  • Level of openness 0 ☆☆☆
  • Document quality 2 ★★☆

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.

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Amber

  • Level of openness 0 ☆☆☆
  • Document quality 3 ★★★

Program package for molecular dynamics simulation. This package includes various material parameters such as peptides, proteins, nuclear acids, carbohydrates, ligands etc., and can perform molecular dynamics simulation of biological macromolecule and cells. This package consists of software for input preparation, simulation, and analysis of results, and is widely used in pharmacy and biological science.

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