Protocols for Molecular Dynamics Simulations of RNA Nanostructures

  • Taejin Kim
  • Wojciech K. Kasprzak
  • Bruce A. ShapiroEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1632)


Molecular dynamics (MD) simulations have been used as one of the main research tools to study a wide range of biological systems and bridge the gap between X-ray crystallography or NMR structures and biological mechanism. In the field of RNA nanostructures, MD simulations have been used to fix steric clashes in computationally designed RNA nanostructures, characterize the dynamics, and investigate the interaction between RNA and other biomolecules such as delivery agents and membranes.

In this chapter we present examples of computational protocols for molecular dynamics simulations in explicit and implicit solvent using the Amber Molecular Dynamics Package. We also show examples of post-simulation analysis steps and briefly mention selected tools beyond the Amber package. Limitations of the methods, tools, and protocols are also discussed. Most of the examples are illustrated for a small RNA duplex (helix), but the protocols are applicable to any nucleic acid structure, subject only to the computational speed and memory limitations of the hardware available to the user.

Key words

RNA Molecular dynamics simulations Force field Antechamber MM-PB(GB)SA Generalized born Elastic network model 



This project has been funded in part with federal funds from the Frederick National Laboratory for Cancer Research, National Institutes of Health, under contract HHSN261200800001E for W.K.K. and E.B. This research was supported in part by the Intramural Research Program of the NIH, National Cancer Institute, Center for Cancer Research. The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services, nor does the mention of trade names, commercial products, or organizations imply endorsement by the US Government.


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Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  • Taejin Kim
    • 1
  • Wojciech K. Kasprzak
    • 2
  • Bruce A. Shapiro
    • 3
    Email author
  1. 1.Department of ChemistryNew York UniversityNew YorkUSA
  2. 2.Basic Science Program, Leidos Biomedical Research, Inc.Frederick National Laboratory for Cancer ResearchFrederickUSA
  3. 3.RNA Structure and Design Section, RNA Biology LaboratoryNational Cancer Institute, National Institutes of HealthFrederickUSA

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