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Photo Mikael Lund

Mikael Lund

Professor

Photo Mikael Lund

FAUNUS: An object oriented framework for molecular simulation

Author

  • Mikael Lund
  • Martin Trulsson
  • Björn Persson

Summary, in English

BACKGROUND: We present a C++ class library for Monte Carlo simulation of molecular systems, including proteins in solution. The design is generic and highly modular, enabling multiple developers to easily implement additional features. The statistical mechanical methods are documented by extensive use of code comments that - subsequently - are collected to automatically build a web-based manual. RESULTS: We show how an object oriented design can be used to create an intuitively appealing coding framework for molecular simulation. This is exemplified in a minimalistic C++ program that can calculate protein protonation states. We further discuss performance issues related to high level coding abstraction. CONCLUSION: C++ and the Standard Template Library (STL) provide a high-performance platform for generic molecular modeling. Automatic generation of code documentation from inline comments has proven particularly useful in that no separate manual needs to be maintained.

Department/s

  • Computational Chemistry

Publishing year

2008

Language

English

Publication/Series

Source Code for Biology and Medicine

Volume

3

Document type

Journal article

Publisher

BioMed Central (BMC)

Topic

  • Theoretical Chemistry (including Computational Chemistry)

Keywords

  • C++
  • proteins
  • monte carlo simulation

Status

Published

ISBN/ISSN/Other

  • ISSN: 1751-0473