Effective interactions in molecular dynamics simulations of lysozyme solutions

Giuseppe Pellicane () and Lev Sarkisov

The European Physical Journal B: Condensed Matter and Complex Systems, 2014, vol. 87, issue 9, 1-10

Abstract: In this article we explore a problem of effective interactions between two rotationally restrained lysozyme molecules forming a crystal contact in aqueous solution. We perform non-equilibrium molecular dynamics simulations in order to estimate the interaction energy as a function of the distance between the two proteins obtained from direct application of the Jarzynski equality (JE), and compare it with that calculated by means of another non-equilibrium approach (Forward-Reverse method) and constrained force methods. The performance of the JE equality when applied to solvated protein interactions is discussed. All of the equilibrium and non-equilibrium methods show clear evidence that the potentials of mean force (PMF) are short-ranged, do not exceed few kTs, and that there is an accumulation of anions in the presence of hydrophobic surfaces. Copyright EDP Sciences, SIF, Springer-Verlag Berlin Heidelberg 2014

Keywords: Statistical and Nonlinear Physics (search for similar items in EconPapers)
Date: 2014
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Persistent link: https://EconPapers.repec.org/RePEc:spr:eurphb:v:87:y:2014:i:9:p:1-10:10.1140/epjb/e2014-50376-9

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DOI: 10.1140/epjb/e2014-50376-9

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