MARBLE

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

An open-source application for molecular dynamics to simulate biopolymers such as proteins and nuclear acids. This application can perform high-speed molecular dynamics simulation by hybrid parallel computing maintaining high-accuracy energy conservation. This application also support high-speed calculation of long-range interaction based on the particle mesh Ewald method. The code is released under GPL lisense.

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Flexible DM-NRG

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

An application for numerical renormalization group calculations. This application can solve magnetic impurity problems described by the Kondo model and the Anderson model. Input files are prepared for typical impulity models. By modifying input files, one can study more general models of the magnetic impurity problems. A mathematica program for generation of input files are also included.

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Elk

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

An open-source application for the first-principles calculation by the all-electron calculation method based on plane wave bases. In addition to standard methods (LDA, GGA, etc.), the LDA+U method, treatment of spin-orbit interaction (noncolinear magnetism), and calculation of phonons are supported. Hybrid parallel computing by OpenMP and MPI is also supported.

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MateriApps Installer

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

A collection of shell scripts for installing open-source applications and tools for computational materials science to macOS, Linux PC, cluster workstations, and major supercomputer systems in Japan. Major applications are preinstalled to the nation-wide joint-use supercomputer system at Institute for Solid State Physics, University of Tokyo by using MateriApps Installer.

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ERmod

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

ERmod is software for calculating the free energy in soft, molecular aggregate. This program rapidly and accurately calculates the free energy of binding of a molecule in the aggregate through combination of the molecular dynamics simulation and the energy-representation theory of solvation. The solubility of a molecule can be determined with ERmod in arbitrary solvent including supercritical fluid and ionic liquid. Assessment is also possible for the binding strength and site of a molecule in micelle, lipid membrane or protein.

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MateriApps LIVE!

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

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.

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Harlem

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

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.

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CASINO

  • Level of openness 3 ★★★
  • Document quality 1 ★☆☆

An open-source application for electronic structure calculation based on the diffusion Monte Carlo method. By using output of other packages of first-principles quantum-chemical calculation, this package performs electronic structure calculation with high accuracy. Although its computational cost is high, various physical quantities can be evaluated very accurately. It implements an efficient parallelization algorithm, and supports massively parallel computing.

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NAMD

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

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.

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FMO in GAMESS

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

The fragment molecular orbital (FMO) method can efficiently do quantum-mechanical calculations of large molecular systems by splitting the whole system into small fragments. The FMO program is distributed within quantum-chemical program suite GAMESS-US. FMO can provide various information regarding the structure and function of biopolymers, such as the interaction between a protein and a ligand.

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