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The principles are illustrated using fluorescence and circular dichroism measurements, and can be applied to other analytical techniques or be adapted with minor modifications for use with other proteins.This chapter contributes a short tutorial on the preparation of molecular dynamics (MD) simulations for a peptide in solution at the interface of an uncoated gold nanosurface. Specifically, the step-by-step procedure will give guidance to set up the simulation of a 16 amino acid long antimicrobial peptide on a gold layer using the program
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