A Hybrid Explicit/Implicit Solvent Technique for Biomolecular Simulations

NOTICES Disclaimers The findings in this report are not to be construed as an official Department of the Army position unless so designated by other authorized documents. Citation of manufacturer's or trade names does not constitute an official endorsement or approval of the use thereof. Destroy this report when it is no longer needed. Do not return it to the originator. Approved for public release; distribution is unlimited. Public reporting burden for this collection of information is estimated to average 1 hour per response, including the time for reviewing instructions, searching existing data sources, gathering and maintaining the data needed, and completing and reviewing the collection information. Send comments regarding this burden estimate or any other aspect of this collection of information, including suggestions for reducing the burden, Respondents should be aware that notwithstanding any other provision of law, no person shall be subject to any penalty for failing to comply with a collection of information if it does not display a currently valid OMB control number. In this work, we design and use a new biomolecular simulation technique that combines explicit solvent molecules and implicit solvent theory. We employ a multigrid approach to speed up the computationally expensive long-range electrostatic energy terms ubiquitous to the classical simulation of biomolecules. It is shown that the multigrid technique affords an order-of-magnitude speedup over conventional cutoff approaches. Our algorithm makes possible a new class of biomolecular simulations that was previously untenable (i.e., the calculation of solvation energies of entire proteins using explicit water molecules). We present comparisons of protein solvation energies obtained from our method and a popular implicit solvent model.