Chapter 5. The Use of Molecular Dynamics Simulations for Modelling Nucleic Acids
- Professor Julia M. Goodfellow
Published Online: 19 DEC 2007
DOI: 10.1002/9783527615339.ch5
Copyright © 1995 VCH Verlagsgesellschaft mbH
Book Title
Computer Modelling in Molecular Biology
Additional Information
How to Cite
Westhof, E., Rubin-Carrez, C. and Fritsch, V. (2007) The Use of Molecular Dynamics Simulations for Modelling Nucleic Acids, in Computer Modelling in Molecular Biology (ed J. M. Goodfellow), Wiley-VCH Verlag GmbH, Weinheim, Germany. doi: 10.1002/9783527615339.ch5
Editor Information
Department of Crystallography, Birkbeck College, University of London, Malet Street, London WClE 7HX, United Kingdom
Publication History
- Published Online: 19 DEC 2007
- Published Print: 27 JUL 1995
ISBN Information
Print ISBN: 9783527300624
Online ISBN: 9783527615339
- Summary
- Chapter
- References
Keywords:
- molecular dynamics simulations;
- nucleic acids;
- potential energy function;
- treatment of solvent;
- counterions
Summary
This chapter contains sections titled:
Introduction
Relevance of Molecular Dynamics Simulations
Water: An Integral Part of Nucleic Acids
Potential Energy Function
Implicit Treatment of the Solvent
Explicit Treatment of the Solvent
Choice of the Ensemble
Choice of Cut-Offs
Choice of Counterions
MD of DNA Oligomers with Implicit Solvent Treatment
MD of DNA Oligomers with Explicit Solvent Treatment
MD of the Anticodon Hairpin with Implicit Solvent Treatment
MD of the Anticodon Hairpin with Explicit Solvent Treatment
Modelling of Large Nucleic Acid Molecules
Conclusions