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Test of molecular dynamics force fields in gramicidin A

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Abstract

The force fields commonly used in molecular dynamics simulations of proteins are optimized under bulk conditions. Whether the same force fields can be used in simulations of membrane proteins is not well established, although they are increasingly being used for such purposes. Here we consider ion permeation in the gramicidin A channel as a test of the AMBER force field in a membrane environment. The potentials of mean force for potassium ions are calculated along the channel axis and compared with the one deduced from the experimental conductance data. The calculated result indicates a rather large central barrier similar to those obtained from other force fields, which are incompatible with the conductance data. We suggest that lack of polarizability is the most likely cause of this problem, and, therefore, urge development of polarizable force fields for simulations of membrane proteins.

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Acknowledgements

This work was supported by grants from the Australian Research Council. The MD simulations were performed using the APAC and AC3 high-performance computing facilities in Australia.

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  1. School of Physics, University of Sydney, NSW, 2006, Australia

    Turgut Bastug & Serdar Kuyucak

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  1. Turgut Bastug
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  2. Serdar Kuyucak
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Correspondence to Turgut Bastug.

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Bastug, T., Kuyucak, S. Test of molecular dynamics force fields in gramicidin A. Eur Biophys J 34, 377–382 (2005). https://doi.org/10.1007/s00249-005-0463-2

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