RESUMO
MiMiC is a framework for performing multiscale simulations in which loosely coupled external programs describe individual subsystems at different resolutions and levels of theory. To make it highly efficient and flexible, we adopt an interoperable approach based on a multiple-program multiple-data (MPMD) paradigm, serving as an intermediary responsible for fast data exchange and interactions between the subsystems. The main goal of MiMiC is to avoid interfering with the underlying parallelization of the external programs, including the operability on hybrid architectures (e.g., CPU/GPU), and keep their setup and execution as close as possible to the original. At the moment, MiMiC offers an efficient implementation of electrostatic embedding quantum mechanics/molecular mechanics (QM/MM) that has demonstrated unprecedented parallel scaling in simulations of large biomolecules using CPMD and GROMACS as QM and MM engines, respectively. However, as it is designed for high flexibility with general multiscale models in mind, it can be straightforwardly extended beyond QM/MM. In this article, we illustrate the software design and the features of the framework, which make it a compelling choice for multiscale simulations in the upcoming era of exascale high-performance computing.
RESUMO
We present a fully self-consistent polarizable embedding (PE) model that does not suffer from unphysical boundary polarization. This is achieved through the use of the minimum-image convention (MIC) in the induced electrostatics. It is a simple yet effective approach that includes a more physically accurate description of the polarization throughout the molecular system. Using PE with MIC (PE-MIC), we shed new light on the limitations of commonly employed cutoff models, such as the droplet model, when used in PE calculations. Specifically, we investigate the effects of the unphysical polarization at the outer boundary by comparing induced dipoles and the associated electrostatic potentials, as well as some optical properties of solute-solvent and biomolecular systems. We show that the magnitude of the inaccuracies caused by the unphysical polarization depends on multiple parameters: the nature of the quantum subsystem and of the environment, the cutoff model and distance, and the calculated property.
RESUMO
The 1H NMR chemical shift of water exhibits non-monotonic dependence on the composition of an aqueous mixture of 1-butyl-3-methylimidazolium chloride, [C4mim][Cl], ionic liquid (IL). A clear minimum is observed for the 1H NMR chemical shift at a molar fraction of the IL of 0.34. To scrutinize the molecular mechanism behind this phenomenon, extensive classical molecular dynamics simulations of [C4mim][Cl] IL and its mixtures with water were carried out. A combined quantum mechanics/molecular mechanics approach based on the density functional theory was applied to predict the NMR chemical shifts. The proliferation of strongly hydrogen-bonded complexes between chloride anions and water molecules is found to be the reason behind the increasing 1H NMR chemical shift of water when its molar fraction in the mixture is low and decreasing. The model shows that the chemical shift of water molecules that are trapped in the IL matrix without direct hydrogen bonding to the anions is considerably smaller than the 1H NMR chemical shift predicted for the neat water. The structural features of neat IL and its mixtures with water have also been analyzed in relation to their NMR properties. The 1H NMR spectrum of neat [C4mim][Cl] was predicted and found to be in very reasonable agreement with the experimental data. Finally, the experimentally observed strong dependence of the chemical shift of the proton at position 2 in the imidazolium ring on the composition of the mixture was rationalized.