Structural Biology Software Database
Structural Biology Software Database

Application Index Record

Category: Molecular Dynamics
Last Update: 01-23-2001

The Molecular Modelling Toolkit (MMTK) is an Open Source program library for molecular simulation applications. In addition to providing ready-to-use implementations of standard algorithms, MMTK serves as a code basis that can be easily extended and modified to deal with standard and non-standard problems in molecular simulations. MMTK is developed in and around Python, a high-level object-oriented general-purpose programming language. In fact, MMTK consists of nothing more than a collection of Python modules, most of which written in Python itself, with only a small time-critical part (e.g. energy evaluation) written in C. MMTK applications are Python programs that make use of these modules. Python was chosen because it allows rapid code development and testing, while providing a very convenient C interface for dealing with time-critical calculations. MMTK is based on an object-oriented model of molecular systems. A system is made up of atoms, molecules, and complexes, all of which are defined in MMTKs chemical database. A molecule, for example, is defined in terms of atoms, functional groups, bonds, force field parameters, etc. It is possible to introduce specialized versions of these objects; for example, MMTK has special support for proteins, which are basically chemical complexes, but can be handled in terms of peptide chains, residues, sidechains etc.


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