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Testing procedures for extracting fluctuation spectra from lipid bilayer simulations.

To address concerns about how to obtain the height-height spectrum from simulations of biomembranes, we emulated the fluctuations in real space using exact input spectra. Two different methods that have given different results in the literature were then used to extract spectra from the emulated fluctuations that were then compared to the exact input spectra. A real space method shows systematic, but small deviations attributed to splines introducing an artifactual filter. A direct Fourier method obtains accurate results when the in-plane placement of the emulated particles is uncorrelated with the out-of-plane undulations, but systematic underestimates occur when the particle placement is more realistically correlated with the undulations. Although quantitative corrections cannot be estimated from our one-dimensional model, the results are qualitatively consistent with the direct Fourier method underestimating the 1/q(2) spectral dependence that is characteristic of a tilt degree of freedom in simulations.