Abstract
Molecular dynamics simulations are increasingly used to characterize static and dynamic processes in large biological systems such as organelles or virions, with the ultimate goal of simulating a whole cell. Programs for constructing the initial coordinates of the envelope as well as packing the interior with proteins and small molecules exist. However, generating input parameters and realistic coordinates for more flexible macromolecules such as DNA, RNA, or carbohydrates, especially close to all-atom resolution, is less routinely done.
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