Coarse-Graining ddCOSMO through an Interface between Tinker and the ddX Library

The Journal of Physical Chemistry B, vol. 126, pp. 8827–8837

Abstract

The domain decomposition conductor-like screening model is an efficient way to compute the solvation energy of solutes within a polarizable continuum medium in a linear scaling computational time. Despite its efficiency, the application to very large systems is still challenging. A possibility to further accelerate the algorithm is resorting to coarse-graining strategies. In this paper we present a preliminary interface between the molecular dynamics package Tinker and the ddX library. The interface was used to test a united atom coarse-graining strategy that allowed us to push ddCOSMO to its limits by computing solvation energies on systems with up to 7 million atoms. We first present benchmarks to find an optimal discretization, and then, we discuss the performance and results obtained with fine- and coarse-grained solvation energy calculations.

Authors 4

1. Michele Nottoli

   University of Pisa

   Affiliation as printed

   Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124Pisa, Italy

2. Aleksandr Mikhalev Aachen Department of Mathematics

   RWTH Aachen University

   Affiliation as printed

   Department of Mathematics, RWTH Aachen University, Schinkelstr. 2, 52062Aachen, Germany

3. Benjamin Stamm Aachen Department of Mathematics

   RWTH Aachen University

   Affiliation as printed

   Department of Mathematics, RWTH Aachen University, Schinkelstr. 2, 52062Aachen, Germany

4. Filippo Lipparini corresponding

   University of Pisa

   Affiliation as printed

   Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124Pisa, Italy