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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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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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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RISMiCal

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

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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GASP

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

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.

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feram

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

A fast molecular dynamics simulator for ferroelectrics. This simulator can execute molecular dynamics calculations quickly by dealing with dipole interaction efficiently. It can simulate the physical property of microscopic ferroelectric thin film of tens of nanometers, which is important in FeRAM(Ferroelectric Random Access Memory), controlling the shapes and effects of inactivated layers.

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NAP

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

A group of applications that perform molecular dynamics, hybrid quantum/classical mechanical simulation, search of chemical reaction path by the nudged elastic band method, and potential parameter fitting. The molecular dynamics code includes interatomic potentials for several metals and semiconductors, and is capable of parallel computation based of spatial decomposition.

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CrySPY

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

CrySPY is a crystal structure prediction tool by utilizing first-principles calculations and a classical MD program. Only by inputting chemical composition, crystal structures can be automatically generated and searched. In ver. 0.6.1, random search, Bayesian optimization, and LAQA are available as searching algorithms. CrySPY is interfaced with VASP, Quantum ESPRESSO, and LAMMPS.

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GENESIS

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

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.

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PolyParGen

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

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.

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