Constant pH Coarse-Grained Molecular Dynamics with Stochastic Charge Neutralization.

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.

SUBMITTER: van Teijlingen A 

PROVIDER: S-EPMC9109222 | biostudies-literature | 2022 May

REPOSITORIES: biostudies-literature