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MoSGrid: efficient data management and a standardized data exchange format for molecular simulations in a grid environment

  • Georg Birkenheuer1,
  • Dirk Blunk2,
  • Sebastian Breuers2,
  • André Brinkmann1,
  • Ines dos Santos Vieira3,
  • Gregor Fels1,
  • Sandra Gesing4,
  • Richard Grunzke5,
  • Sonja Herres-Pawlis3,
  • Oliver Kohlbacher4Email author,
  • Jens Krüger1,
  • Ulrich Lang2,
  • Lars Packschies2,
  • Ralph Müller-Pfefferkorn5,
  • Patrick Schäfer6,
  • Thomas Steinke6,
  • Klaus-Dieter Warzecha2 and
  • Martin Wewior2
Journal of Cheminformatics20124(Suppl 1):P21

Published: 1 May 2012


File SystemMolecular SimulationExchange FormatData RepositoryGrid Environment

The MoSGrid (Molecular Simulation Grid) project is currently establishing a platform that aims to be used by both experienced and inexperienced researchers to submit molecular simulation calculations, monitor their progress, and retrieve the results. It provides a web-based portal to easily set up, run, and evaluate molecular simulations carried out on D-Grid resources. The range of applications available encompasses quantum chemistry, molecular dynamics, and protein-ligand docking codes.

In addition, data repositories were developed, which contain the results of calculations as well as “recipes” or workflows. These can be used, improved, and distributed by the users. A distributed high-throughput file system allows efficient access to large amounts of data in the repositories. For storing both the input and output of the calculations, we have developed MSML (Molecular Simulation Markup Language), a CML derivative (Chemical Markup Language). MSML has been designed to store structural information on small as well as large molecules and results from various molecular simulation tools and docking tools. It ensures interoperability of different tools through a consistent data representation.

At the new platform is already available to the scientific community in a beta test phase. Currently, portlets for generic workflows, Gaussian, and Gromacs applications are publicly accessible [1, 2].

Authors’ Affiliations

Universität Paderborn, Paderborn, Germany
Universität zu Köln, Köln, Germany
Fakultät Chemie, Technische Universität Dortmund, Dortmund, Germany
Eberhard-Karls-Universität Tübingen, Tübingen, Germany
Technische Universität Dresden, Dresden, Germany
Konrad-Zuse-Zentrum für Informationstechnik, Berlin, Germany


  1. Gesing , et al: A Science Gateway for Molecular Simulations. EGI User Forum 2011. 2011, 94-95. Book of Abstracts, 978 90 816927 1 7Google Scholar
  2. Gesing , et al: Granular Security for a Science Gateway in Structural Bioinformatics. IWSG-Life 2011 (International Workshop on Science Gateways for Life Sciences). 2011, London, UKGoogle Scholar


© Birkenheuer et al; licensee BioMed Central Ltd. 2012

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.