Eur. Phys. J. B (2014) 87: 191
https://doi.org/10.1140/epjb/e2014-50376-9

Regular Article

Effective interactions in molecular dynamics simulations of lysozyme solutions

¹ School of Chemistry and Physics, University of Kwazulu-Natal, Private Bag X01, Scottsville 3209, Pietermaritzburg, South Africa
² National Institute for Theoretical Physics (NITheP), KZN node, Pietermaritzburg, South Africa
³ Institute for Materials and Process, School of Engineering, The University of Edinburgh, EH9 3JL, UK

^a e-mail: pellicane@ukzn.ac.za

Received: 9 June 2014
Received in final form: 1 July 2014
Published online: 1 September 2014

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.