Abstract

By analogy with single-molecule pulling experiments, we present a computational framework to obtain free energy differences between complex solvation states. To illustrate our approach, we focus on the calculation of solvation free energies (SFEs). However, the method can be readily extended to cases involving more complex solutes and solvation conditions as well as to the calculation of binding free energies. The main idea is to drag the solute across the simulation box where atomistic and ideal gas representations of the solvent coexist at constant temperature and chemical potential. At finite pulling speeds, the resulting work allows one to extract SFEs via nonequilibrium relations, whereas at infinitely slow pulling speeds, this process becomes equivalent to the thermodynamic integration method. Results for small molecules well agree with literature data and pave the way to systematic studies of arbitrarily large and complex molecules.

Highlights

  • P2i /2mi the total kinetic energy of the system

  • The vector R is the position of the center of mass of a given molecule, and the switching field λ(R), which determines the molecule’s identity, takes the value 1 if the molecule is in the atomistic region (AT), 0 is in the ideal gas region (IG), and a smooth interpolation between these values is defined in the hybrid (HY) region

  • This potential drives the solute molecule across the simulation box to sample different solvation conditions between two extreme cases: a fully solvated solute and its gas phase

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Summary

Introduction

P2i /2mi the total kinetic energy of the system. In this particular case, we write the scitation.org/journal/jcp potential energy as. We select a water molecule inside the AT region (schematically indicated in Fig. 1) and restrain the x-coordinate of its oxygen atom using the harmonic potential in Eq (4) with zero pulling rate and spring constant κ = 209.2 kJ/mol/Å2. We perform 20 uncorrelated simulation runs to calculate the solvation free energy profile and shift it with respect to the IG region.

Results
Conclusion
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