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Lipid Converter, A Framework for Lipid Manipulations in Molecular Dynamics Simulations

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Abstract

Construction of lipid membrane and membrane protein systems for molecular dynamics simulations can be a challenging process. In addition, there are few available tools to extend existing studies by repeating simulations using other force fields and lipid compositions. To facilitate this, we introduce Lipid Converter, a modular Python framework for exchanging force fields and lipid composition in coordinate files obtained from simulations. Force fields and lipids are specified by simple text files, making it easy to introduce support for additional force fields and lipids. The converter produces simulation input files that can be used for structural relaxation of the new membranes.

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Acknowledgments

We thank Matt Eckler for beta-testing Lipid Converter.

Conflict of interest

None declared.

Funding

This work was supported by an European Union fellowship (Marie Curie) PIOF-GA-2010-275548 to PL and NIH Grant RO1GM098304 to PK.

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Authors and Affiliations

  1. Departments of Molecular Physiology and Biological Physics and Biomedical Engineering, University of Virginia, Charlottesville, VA, 22908, USA

    Per Larsson & Peter M. Kasson

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  1. Per Larsson
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  2. Peter M. Kasson
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Correspondence to Peter M. Kasson.

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Larsson, P., Kasson, P.M. Lipid Converter, A Framework for Lipid Manipulations in Molecular Dynamics Simulations. J Membrane Biol 247, 1137–1140 (2014). https://doi.org/10.1007/s00232-014-9705-5

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  • DOI: https://doi.org/10.1007/s00232-014-9705-5

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