Constant pH coarse-grained molecular dynamics with stochastic charge neutralization

van Teijlingen, Alexander and Swanson, Hamish W. A. and Lau, King Hang Aaron and Tuttle, Tell (2022) Constant pH coarse-grained molecular dynamics with stochastic charge neutralization. Journal of Physical Chemistry Letters, 13 (18). 4046−4051. ISSN 1948-7185 (https://doi.org/10.1021/acs.jpclett.2c00544)

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Abstract

pH dependence abounds in biochemical systems; however, many simulation methods used to investigate these systems do not consider this property. Using a modified version of the hybrid non-equilibrium molecular dynamics (MD)/Monte Carlo algorithm, we include a stochastic charge neutralization method, which is particularly suited to the MARTINI force field and enables artifact-free Ewald summation methods in electrostatic calculations. We demonstrate the efficacy of this method by reproducing pH-dependent self-assembly and self-organization behavior previously reported in experimental literature. In addition, we have carried out experimental oleic acid titrations where we report the results in a more relevant way for the comparison with computational methods than has previously been done.

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