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.
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Acknowledgments
This work was supported financially by DSTL (T.J.P.) and a Rutherford Discovery Fellowship (15-MAU-001) and Marsden grant (15-UOA-105) (J.R.A.).
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Collier, T.A., Piggot, T.J., Allison, J.R. (2020). Molecular Dynamics Simulation of Proteins. In: Gerrard, J., Domigan, L. (eds) Protein Nanotechnology. Methods in Molecular Biology, vol 2073. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9869-2_17
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