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This article is part of the supplement: 7th German Conference on Chemoinformatics: 25 CIC-Workshop

Open Access Poster presentation

The GMX-Plugin for the CELLmicrocosmos MembraneEditor

Sebastian Rubert1, Christian Gamroth1, André J Heissmann1, Gunther Lukat1, Ralf Rotzoll1, Alexander Schäfer1, Jens Krüger2 and Björn Sommer1*

Author Affiliations

1 Bio-/Medical Informatics Department, Bielefeld University, Bielefeld, NRW, 33615, Germany

2 Department of Chemistry, University of Paderborn, Paderborn, NRW, 33098, Germany

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Journal of Cheminformatics 2012, 4(Suppl 1):P49  doi:10.1186/1758-2946-4-S1-P49

The electronic version of this article is the complete one and can be found online at: http://www.jcheminf.com/content/4/S1/P49


Published:1 May 2012

© 2012 Rubert et al; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Poster presentation

Membrane research in silico can roughly be subdivided into three parts: the modeling, simulation and analysis process. The GMX-plugin tries to bridge the gap between these three parts represented by the tools CELLmicrocosmos MembraneEditor (CmME) and Gromacs (GMX).

CmME was developed to enable students and researchers a generation of PDB-based membranes in a fast and intuitive way without high computational requirements. From the beginning it was developed as an independent Javabased web start tool with a user-interface providing direct access to all functions implemented. The high performance of most Membrane Packing Algorithms is achieved especially by the handling of molecules as inflexible structures. The generated membranes can be exported to a PDB-file to be used with external applications [1].

One of these programs is GMX (here version 4.5.X), the well-known Molecular Dynamics package, supported and used over one decade by a very large community. It is applicable to the simulation of peptides, proteins, lipids as well as complete membranes [2].

The GMX-plugin version 1.1 is intended as an interface between CmME and GMX. It is combined with CmME on the local system and is able to access GMX on a local machine or on an external high-performance system via ssh or Unicore [3]. It is packaged with a set of lipids compatible to the Gromos 45a3 forcefield. In addition, predefined protocols exist for immediately starting a simulation of CmME-generated membranes. Custom protocols may be created, saved and reloaded by the user.

The beta version of the plugin can be downloaded at: http://Cm2.CELLmicrocosmos.org webcite.

References

  1. Sommer B, Dingersen T, Gamroth C, Schneider S, Rubert S, Krüger J, Dietz K-J: CELLmicrocosmos 2.2 MembraneEditor: A Modular Interactive Shape-Based Software Approach To Solve Heterogeneous Membrane Packing Problems.

    J Chem Inf Model 2011, 51:1165-1182. OpenURL

  2. Gromacs 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation

    J Chem Theory Comput 2008, 4:435-447. Publisher Full Text OpenURL

  3. Schuller B, Schumacher M: Space-Based Approach to High-Throughput Computations in UNICORE 6 Grids.

    Lect Notes Comput Sc 2009, 5415:75-83. Publisher Full Text OpenURL