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Protocol for Molecular Dynamics Simulations of Proteins   

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Original research article

A brief version of this protocol appeared in:
BMC Genomics
Oct 2013

Abstract

Molecular dynamics (MD) simulations have become one of the most important tools in understanding the behavior of bio-molecules on nanosecond to microsecond time scales. In this protocol, we provide a general approach and standard setup protocol for MD simulations by using the Gromacs MD suite.

Keywords: Molecular dynamics simulations, Conformational studies, Gromacs, Structural studies, Protein dynamics

Background

While molecular dynamics (MD) simulations are increasingly getting popular in studying protein dynamics in silico, there is a strong need to correlate the results with experimental observations. It is necessary that the protein model and the chosen environment for the simulations should mimic the native environment as close as possible. In general, there are three key stages in molecular dynamics simulations: Setup, production run, and analysis of the trajectories. The setup includes the input structures, parameters, force-fields and topologies. However, the readymade setup and wrong parameters could adversely affect the outcome making a false assessment of the biological interpretation. In view of a manual setup as a better choice to setup simulations, we through this protocol, provide a general approach and standard setup protocol for MD simulations. Many online/offline tools are available to perform MD simulations. One amongst the open source tools is Gromacs (Abraham et al., 2015; Pronk et al., 2013; Van der Spoel et al.,2005), a robust and popular MD simulations suite available today which supports almost all the major force fields. In this protocol we also refer to simulations of membrane proteins previously performed in vacuum as a temporary alternative to simulations including the membrane.

Copyright: © 2016 The Authors; exclusive licensee Bio-protocol LLC.
How to cite: Gajula, M. P., Kumar, A. and Ijaq, J. (2016). Protocol for Molecular Dynamics Simulations of Proteins. Bio-protocol 6(23): e2051. DOI: 10.21769/BioProtoc.2051.
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