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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