Molecular Dynamics Simulation of Proteins

Thomas A Collier; Thomas J Piggot; Jane R Allison

doi:10.1007/978-1-4939-9869-2_17

Molecular Dynamics Simulation of Proteins

Methods Mol Biol. 2020:2073:311-327. doi: 10.1007/978-1-4939-9869-2_17.

Authors

Thomas A Collier^{1

2}, Thomas J Piggot^{3

4}, Jane R Allison^{5

6

7

8}

Affiliations

¹ Centre for Theoretical Chemistry and Physics, Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand.
² Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand.
³ Chemical, Biological and Radiological Sciences, Defence Science and Technology Laboratory, Wiltshire, UK.
⁴ School of Chemistry, University of Southampton, Southampton, UK.
⁵ Centre for Theoretical Chemistry and Physics, Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand. j.allison@auckland.ac.nz.
⁶ Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand. j.allison@auckland.ac.nz.
⁷ Biomolecular Interaction Centre, University of Canterbury, Auckland, New Zealand. j.allison@auckland.ac.nz.
⁸ School of Biological Sciences, University of Auckland, Auckland, New Zealand. j.allison@auckland.ac.nz.

PMID: 31612449
DOI: 10.1007/978-1-4939-9869-2_17

Abstract

Molecular dynamics simulations allow the conformational motion of a molecule such as a protein to be followed over time at atomic-level detail. Several choices need to be made prior to running a simulation, including the software, which molecules to include in the simulation, and the force field used to describe their behavior. Guidance on making these choices and other important aspects of running MD simulations is outlined here.

Keywords: Force field; Molecular dynamics; Proteins.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Computational Biology
Molecular Dynamics Simulation*
Proteins / chemistry*
Proteins / ultrastructure
Software

Substances

Proteins