Analysis of the influence of simulation parameters on biomolecule-linked water networks.

ABSTRACT

Advancement of computational molecular dynamics allows rapid calculation of large biomolecular systems in their water surroundings. New approaches of prediction of hydration networks of biomolecular surfaces and complex interfaces are also based on molecular dynamics (MD). Calculations with explicit solvent models can trace thousands of water molecules individually on a real time scale, yielding information on their mobility, and predicting their networking with biomolecular solutes and other water partners. Here, we investigate the effect of key parameters of molecular dynamics simulations on the quality of such predictions. Accordingly, systematic scans on temperature, pressure, force field, explicit water model and thermodynamic ensemble are performed. Explanations of optimal parameter values are provided using structural examples and analyses of the corresponding hydration networks.