Biomolecular Simulations

Methods and Protocols

  • Luca Monticelli
  • Emppu Salonen

Part of the Methods in Molecular Biology book series (MIMB, volume 924)

Table of contents

  1. Front Matter
    Pages i-xiii
  2. Quantum Mechanics Calculations

    1. Front Matter
      Pages 1-1
    2. Mikael P. Johansson, Ville R. I. Kaila, Dage Sundholm
      Pages 3-27
    3. Kari Laasonen
      Pages 29-42
    4. Gerrit Groenhof
      Pages 43-66
    5. Alessio Lodola, Adrian J. Mulholland
      Pages 67-89
    6. Thomas Steinbrecher, Marcus Elstner
      Pages 91-124
  3. Classical Mechanics: Atomistic Simulations

    1. Front Matter
      Pages 125-125
    2. Susanna Hug
      Pages 127-152
    3. Ayori Mitsutake, Yoshiharu Mori, Yuko Okamoto
      Pages 153-195
    4. Luca Monticelli, D. Peter Tieleman
      Pages 197-213
    5. Hanne S. Antila, Emppu Salonen
      Pages 215-241
    6. G. Andrés Cisneros, Volodymyr Babin, Celeste Sagui
      Pages 243-270
    7. Michael R. Shirts, David L. Mobley
      Pages 271-311
    8. Mahmoud Moradi, Volodymyr Babin, Celeste Sagui, Christopher Roland
      Pages 313-337
    9. Andrea Bortolato, Marco Fanton, Jonathan S. Mason, Stefano Moro
      Pages 339-360
    10. Giray Enkavi, Jing Li, Paween Mahinthichaichan, Po-Chao Wen, Zhijian Huang, Saher A. Shaikh et al.
      Pages 361-405
    11. Svetlana Baoukina, D. Peter Tieleman
      Pages 431-444
    12. Nicolas Foloppe, Marc Guéroult, Brigitte Hartmann
      Pages 445-468
    13. Nicolas Sapay, Alessandra Nurisso, Anne Imberty
      Pages 469-483
  4. Mesoscopic Simulations and Coarse-grained Models

    1. Front Matter
      Pages 485-485
    2. Xavier Periole, Siewert-Jan Marrink
      Pages 533-565
    3. Matej Praprotnik, Luigi Delle Site
      Pages 567-583
    4. Zhong-Yuan Lu, Yong-Lei Wang
      Pages 617-633
    5. Syma Khalid, Peter J. Bond
      Pages 635-657
  5. Back Matter
    Pages 699-702

About this book


Over the past 40 years the field of molecular simulations has evolved from picosecond studies of isolated macromolecules in vacuum to studies of complex, chemically heterogeneous biological systems consisting of millions of atoms, with the simulation time scales spanning up to milliseconds. In Biomolecular Simulations: Methods and Protocols, expert researchers illustrate many of the methods commonly used in molecular modelling of biological systems, including methods for electronic structure calculations, classical molecular dynamics simulations and coarse-grained techniques. A selection of advanced techniques and recent methodological developments, which rarely find coverage in traditional textbooks, is also introduced.


Written in the highly successful Methods in Molecular Biology series format, chapters include general introductions to well-established computational methodologies, applications to real-world biological systems, as well as practical tips and general protocols on carrying out biomolecular simulations. Special emphasis is placed on simulations of proteins, lipids, nucleic acids, and carbohydrates. Authoritative and practical, Biomolecular Simulations: Methods and Protocols seeks to aid scientists in further simulation studies of biological systems.


Coarse-graining QM/MM methods ab initio molecular dynamics algorithms biomolecular modelling electronic structure free energy calculations lipid membranes membrane proteins polarizable force fields

Editors and affiliations

  • Luca Monticelli
    • 1
  • Emppu Salonen
    • 2
  1. 1.DSIMB, UMR-S 665INSERMParisFrance
  2. 2., Department of Applied PhysicsAalto UniversityAALTOFinland

Bibliographic information

  • DOI
  • Copyright Information Springer Science+Business Media New York 2013
  • Publisher Name Humana Press, Totowa, NJ
  • eBook Packages Springer Protocols
  • Print ISBN 978-1-62703-016-8
  • Online ISBN 978-1-62703-017-5
  • Series Print ISSN 1064-3745
  • Series Online ISSN 1940-6029
  • Buy this book on publisher's site