Microsecond Molecular Dynamics Simulations of Proteins Using a Quasi-Equilibrium Solvation Shell Model

Ovchinnikov, Victor; Conti, Simone; Lau, Edmond Y.; Lightstone, Felice C.; Karplus, Martin

doi:10.1021/acs.jctc.9b01072

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Microsecond Molecular Dynamics Simulations of Proteins Using a Quasi-Equilibrium Solvation Shell Model

Ovchinnikov, Victor·Conti, Simone·Lau, Edmond Y.·Lightstone, Felice C.·Karplus, Martin

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Abstract

In this work, we describe the development and implementation of a quasi-equilibrium hydration shell model of biomolecular solvation with adaptive boundaries. Applying the model to microsecond-long molecular dynamics simulations of several protein systems of varying complexity, we find that the model simulation results are of comparable quality to those obtained from simulations of fully solvated systems, but at a reduced computational cost. We discuss the dominant sources of error in the model and outline directions for future improvements.

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37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY Solvents ions molecules peptides and proteins solution chemistry

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Ovchinnikov, Victor, Conti, Simone, Lau, Edmond Y., Lightstone, Felice C., Karplus, Martin. 2020-02-11. Microsecond Molecular Dynamics Simulations of Proteins Using a Quasi-Equilibrium Solvation Shell Model. https://doi.org/10.1021/acs.jctc.9b01072

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