Preparing and Analyzing Polarizable Molecular Dynamics Simulations with the Classical Drude Oscillator Model.

Molecular dynamics (MD) simulations performed with force fields that include explicit electronic polarization are becoming more prevalent in the field. The increasing emergence of these simulations is a result of continual refinement against a range of theoretical and empirical target data, optimization of software algorithms for higher performance, and availability of graphical processing unit hardware to further accelerate the simulations. Polarizable MD simulations are likely to be most impactful in biomolecular systems in which heterogeneous environments or unique microenvironments exist that would lead to inaccuracies in simulations performed with fixed-charge, nonpolarizable force fields. The further adoption of polarizable MD simulations will benefit from tutorial material that specifically addresses preparing and analyzing their unique features. In this chapter, we introduce common protocols for preparing routine biomolecular systems containing proteins, including both a globular protein in aqueous solvent and a transmembrane model peptide in a phospholipid bilayer. Details and example input files are provided for preparation of the simulation system using CHARMM, performing the simulations with OpenMM, and analyzing interesting dipole moment properties in CHARMM.