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The hydroperoxy radical (HO2) plays a critical role in Earth's atmospheric chemistry as a component of many important reactions. The self-reaction of hydroperoxy radicals in the gas phase is strongly affected by the presence of water vapor. In this work, we explore the potential energy surfaces of hydroperoxy radicals hydrogen bonded to one or two water(More)
With improvements in computer speed and algorithm efficiency, MD simulations are sampling larger amounts of molecular and biomolecular conformations. Being able to qualitatively and quantitatively sift these conformations into meaningful groups is a difficult and important task, especially when considering the structure-activity paradigm. Here we present a(More)
The goals of this article are to (1) provide further validation of the Glycam06 force field, specifically for its use in implicit solvent molecular dynamic (MD) simulations, and (2) to present the extension of G.N. Ramachandran's idea of plotting amino acid phi and psi angles to the glycosidic phi, psi, and omega angles formed between carbohydrates. As in(More)
In this contribution, we examine how visualization on an ultra high-resolution display wall can augment force-field research in the field of molecular modeling. Accurate force fields are essential for producing reliable simulations, and subsequently important for several fields of applications (e.g. rational drug design and biomolecular modeling). We(More)
The bacterial ribosome is a major target of naturally occurring thiopeptides antibiotics. Studying thiopeptide (e.g. thiostrepton) binding to the GAR's 23S·L11 ribosomal subunit using docking methods is challenging. Regarding the target, the binding site is composed of a flexible protein-RNA nonbonded interface whose available crystal structure is of medium(More)
In this contribution we introduce the technical concept and implementation details concerning the front end of our force-field optimization workflow package for intramolecular degrees of freedom, called Wolf2Pack. The package's design follows our belief that parameter optimization should be a user-driven, but program guided, workflow with specific modular(More)
In this article we present our recent efforts in designing a comprehensive consistent scientific workflow, nicknamed Wolf 2 Pack, for force-field optimization in the field of computational chemistry. Atomistic force fields represent a mul-tiscale bridge that connects high-resolution quantum mechanics knowledge to coarser molecular mechanics based models.(More)