Abstract
Advances in the field of atomic-level membrane simulations are being driven by continued growth in computing power, improvements in the available potential energy functions for lipids, and new algorithms that implement advanced sampling techniques. These developments are allowing simulations to assess time- and length scales wherein meaningful comparisons with experimental measurements on macroscopic systems can be made. Such comparisons provide stringent tests of the simulation methodologies and force fields, and thus, advance the simulation field by pointing out shortcomings of the models. Extensive testing against available experimental data suggests that for many properties modern simulations have achieved a level of accuracy that provides substantial predictive power and can aid in the interpretation of experimental data. This combination of closely coupled laboratory experiments and molecular dynamics simulations holds great promise for the understanding of membrane systems. In the following, the molecular dynamics method is described with particular attention to those aspects critical for simulating membrane systems and to the calculation of experimental observables from the simulation trajectory.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Verlet, L. (1967) Computer experiments on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules. Phys. Rev. 159, 98–103.
Allen, M. P. and Tildesley, D. J. (1987) Computer Simulation of Liquids, Clarendon, Oxford.
Andersen, H. C. (1980) Molecular dynamics simulations at constant temperature and/or pressure. J. Chem. Phys. 72, 2384–2393.
Nose, S. and Klein, M. L. (1983) Constant pressure molecular dynamics for molecular systems. Mol. Phys. 50, 1055–1076.
Hoover, W. G. (1985) Canonical dynamics: Equillibrium phase-space distributions. Phys. Rev. A 31, 1695–1697.
Feller, S. E., Zhang, Y., Pastor, R. W., and Brooks, B. R. (1995) Constant pressure molecular dynamics simulation: The Langevin piston method. J. Chem. Phys. 103, 4613.
Jahnig, F. (1996) What is the surface tension of a bilayer membrane? Biophys. J. 71, 1348–1349.
Feller, S. E. and Pastor, R. W. (1996) On simulating lipid bilayers with an applied surface tension: periodic boundary conditions and undulations. Biophys. J. 71, 1350–1355.
Lindahl, E. and Edholm, O. (2000) Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations. Biophys. J. 79, 426–433.
Feller, S. E. and Pastor, R. W. (1997) Length scales of lipid dynamics and molecular dynamics. Pac. Symp. Biocomput. 142-150.
Horn, H. W., Swope, W. C., Pitera, J. W., et al. (2004) Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew. J. Chem. Phys. 120, 9665–9679.
Lindahl, E. and Edholm, O. (2000) Spatial and energetic-entropic decomposition of surface tension in lipid bilayers from molecular dynamics simulations. J. Chem. Phys. 113, 3882–3893.
Gullingsrud, J. and Schulten, K. (2004) Lipid bilayer pressure profiles and mechanosensitive channel gating. Biophys. J. 86, 3496–3509.
Carrillo-Tripp, M. and Feller, S. E. (2005) Evidence for a Mechanism by Which Omega-3 Polyunsaturated Lipids May Affect Membrane Protein Function. Biochemistry 44, 10,164–10,169.
Brooks, B. R., Bruccoler, R. E., Olafson, B. D., States, D. J., Swaminathan, S., and Karplus, M. (1983) CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J. Comp. Chem. 4, 187–217.
Schlenkrich, M., Brickmann, J., MacKerell, A. D., Jr., and Karplus, M. (1996) Empirical potential energy function for phospholipids: criteria for parameter optimization and applications, in Biological Membranes: A Molecular Perspective from Computation and Experiment (Merz, K. and Roux, B., eds.), Birkhauser, Boston, pp. 31–81.
Feller, S. E. and MacKerell, A. D., Jr. (2000) An improved empirical potential energy function for molecular simulations of phospholipids. J. Phys. Chem. B 104, 7510–7515.
Klauda, J. B., Brooks, B. R., and Pastor, R. W. (2005) Adjacent gauche stabilization in linear alkanes: implications for polymer models and conformational analysis. J. Phys. Chem. B 109, 15,684–15,686.
Klauda, J. B., Brooks, B. R., MacKerell, A. D., Jr., Venable, R. M., and Pastor, R. W. (2005) An ab Initio Study on the Torsional Surface of Alkanes and Its Effect on Molecular Simulations of Alkanes and a DPPC Bilayer. J. Phys. Chem. B 109, 5300–5311.
Laguee, P., Pastor, R. W., and Brooks, B. R. (2004) Pressure-Based Long-Range Correction for Lennard-Jones Interactions in Molecular Dynamics Simulations: Application to Alkanes and Interfaces. J. Phys. Chem. B 108, 363–368.
Feller, S. E., Yin, D., Pastor, R. W., and MacKerell, A. D., Jr. (1997) Molecular dynamics simulation of unsaturated lipid bilayers at low hydration: parameterization and comparison with diffraction studies. Biophys. J. 73, 2269–2279.
Feller, S. E., Pastor, R. W., Rojnuckarin, A., Bogusz, S., and Brooks, B. R. (1996) Effect of Electrostatic Force Truncation on Interfacial and Transport Properties of Water. J. Phys. Chem. 100, 17,011–17,020.
Patra, M., Karttunen, M., Hyvonen, M. T., Falck, E., Lindqvist, P., and Vattulainen, I. (2003) Molecular Dynamics Simulations of Lipid Bilayers: Major Artifacts Due to Truncating Electrostatic Interactions. Biophys. J. 84, 3636–3645.
Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., and Pedersen, L. G. (1995) A smooth particle mesh Ewald method. J. Chem. Phys. 103, 8577.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2007 Humana Press Inc.
About this protocol
Cite this protocol
Feller, S.E. (2007). Molecular Dynamics Simulations as a Complement to Nuclear Magnetic Resonance and X-Ray Diffraction Measurements. In: Dopico, A.M. (eds) Methods in Membrane Lipids. Methods in Molecular Biology™, vol 400. Humana Press. https://doi.org/10.1007/978-1-59745-519-0_7
Download citation
DOI: https://doi.org/10.1007/978-1-59745-519-0_7
Publisher Name: Humana Press
Print ISBN: 978-1-58829-662-7
Online ISBN: 978-1-59745-519-0
eBook Packages: Springer Protocols