☆ 4.7 Article

Architecture, implementation and parallelisation of the GROMOS software for biomolecular simulation

COMPUTER PHYSICS COMMUNICATIONS (2012)

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Journal

COMPUTER PHYSICS COMMUNICATIONS
Volume 183, Issue 4, Pages 890-903

Publisher

ELSEVIER
DOI: 10.1016/j.cpc.2011.12.014

Keywords

GROMOS; Molecular dynamics; Parallelisation; GPU; Software design

Categories

Computer Science, Interdisciplinary Applications Physics, Mathematical

Funding

  1. National Center of Competence in Research (NCCR) in Structural Biology
  2. Swiss National Science Foundation [200020-121913]
  3. European Research Council [228076]
  4. Swiss National Science Foundation (SNF) [200020-121913] Funding Source: Swiss National Science Foundation (SNF)

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In this work the design of the latest version of the GROMOS software for biomolecular simulation, GROMOS11 is discussed. Detailed organisation and class descriptions of the MD++ simulation program and the GROMOS++ analysis package are given. It is shown how the code was documented, how it can be easily modified and extended, how debugging of it is carried out. Additional efficiency and parallelisation concepts are presented and benchmarked. (C) 2011 Elsevier B.V. All rights reserved.

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