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Simulation Methods - Other Resources

Submitted by site admin on Thu, 2007-02-08 21:46.

Major Code/Work Flow Efforts


CML and Workflow


Software Packages

  • LAMMPS:Large-scale Atomic/Molecular Massively Parallel Simulator, administered by Steve Plimpton at Sandia
  • MCCCS Towhee: Monte Carlo for Complex Chemical Systems, administered by Marcus G. Martin at Sandia
  • GAMGI General Atomistic Modelling Graphic Interface
  • J. Comp. Chem. special issue "...on the methods and applications of molecular simulation in the area of biological systems [with]...manuscripts from the leading authors of large molecular simulation programs- Amber, BOSS/MCPRO, GROMOS, GROMACS, IMPACT, and NAMD- [containing]... an updated description of their programs, the critical algorithms, and force field approaches that form the basis for the methods, and representative applications that illustrate the scope of systems to which these techniques can be applied."
  • MDX: "...a collection of C libraries to enable the development of methods for molecular dynamics of biomolecules...MDX provides a modular approach to developing molecular dynamics software. The goal is to develop reusable modules with well-defined interfaces towards the implementation of a sequential molecular dynamics program and related tools. The priority is to create MD codes that are easy to understand and modify, enabling straightforward design and testing of new methods. Flexible software libraries will provide tools for taking care of common tasks, allowing more rapid development of revolutionary techniques." This is related to NAMD.
  • "MESHI: a new library of Java classes for molecular modeling." N. Kalisman, A. Levi, T. Maximova, D. Reshef, S. Zafriri-Lynn, Y. Gleyzer and C. Keasar. Bioinformatics, 21, 3931-3932 (2005). http://dx.doi.org/10.1093/bioinformatics/bti630 ; http://www.cs.bgu.ac.il/~meshi/
  • ABINIT: ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave basis. ABINIT also includes options to optimize the geometry according to the DFT forces and stresses, or to perform molecular dynamics simulations using these forces, or to generate dynamical matrices, Born effective charges, and dielectric tensors. Excited states can be computed within the Time-Dependent Density Functional Theory (for molecules), or within Many-Body Perturbation Theory (the GW approximation).
  • CAMPOS: The CAMPOS project consists of several atomistic simulation tools and an environment for setting up atomistic calculations and visualizations, written in Python.
  • Ghemical: Ghemical is a computational chemistry software package released under the GNU GPL. It means that full source code of the package is available, and users are free to study and modify the package. Ghemical is written in C++. It has a graphical user interface (which is based on GTK2), and it supports both quantum-mechanics (semi-empirical and ab initio) models and molecular mechanics models (there is an experimental Tripos 5.2-like force field for organic molecules). Also a tool for reduced protein models [1] is included. Geometry optimization, molecular dynamics and a large set of visualization tools are currently available. Ghemical relies on external code to provide the quantum-mechanical calculations. Semi-empirical methods MNDO, MINDO/3, AM1 and PM3 are provided by the MOPAC7 package (Public Domain). The MPQC package (GNU GPL) is used to provide ab initio methods: the methods based on Hartree-Fock theory are currently supported with basis sets ranging from STO-3G to 6-31G**. Ghemical also uses the OpenBabel package for importing and exporting many different file formats (as well as for other tasks).
  • GROMACS: popular MD software for running large-scale simulation.
  • Moscito: software for MD simulations of molecular aggregates. Standard molecular mechanics force-fields such as AMBER, OPLS, CHARMM and GROMOS can be employed. Simulations can be carried out in different ensembles such as NVE, NVT or NPT using the weak coupling scheme. (Smooth Particle Mesh) Ewald summation is used for long range electrostatic interactions.
  • MPQC: MPQC is the Massively Parallel Quantum Chemistry Program. It computes properties of atoms and molecules from first principles using the time independent Schrödinger equation. It runs on a wide range of architectures ranging from individual workstations to symmetric multiprocessors to massively parallel computers. Its design is object oriented, using the C++ programming language.
  • Octopus: octopus is a program aimed at the ab initio virtual experimentation on a hopefully ever increasing range of systems types.
  • PyQuante: PyQuante is an open-source suite of programs for developing quantum chemistry methods. The program is written in the Python programming language, but has many "rate-determining" modules also written in C for speed.


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