Abstract
Non-equilibrium molecular dynamics (NEMD) simulation has been recognized as a powerful tool for examining biomolecules and provides fruitful insights into not only non-equilibrium but also equilibrium processes. We review recent advances in NEMD simulation and relevant, fundamental results of non-equilibrium statistical mechanics. We first introduce Crooks fluctuation theorem and Jarzynski equality that relate free energy difference to work done on a physical system during a non-equilibrium process. The theorems are beneficial for the analysis of NEMD trajectories. We then describe rate theory, a framework to calculate molecular kinetics from a non-equilibrium process; this theoretical framework enables us to calculate a reaction time—mean-first passage time—from NEMD trajectories. We, in turn, present recent NEMD techniques that apply an external force to a system to enhance molecular dissociation and introduce their application to biomolecules. Lastly, we show the current status of an appropriate selection of reaction coordinates for NEMD simulation.
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We thank Prof. Haruki Nakamura for providing us the opportunity to write the review article.
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The authors were supported by JSPS KAKENHI Grant No. 22H00553.
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Iida, S., Tomoshi, K. Free energy and kinetic rate calculation via non-equilibrium molecular simulation: application to biomolecules. Biophys Rev 14, 1303–1314 (2022). https://doi.org/10.1007/s12551-022-01036-3
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DOI: https://doi.org/10.1007/s12551-022-01036-3