Linear scaling computation of forces for the domain-decomposition linear Poisson–Boltzmann method

The Journal of Chemical Physics, vol. 158, pp. 104105

Abstract

The Linearized Poisson-Boltzmann (LPB) equation is a popular and widely accepted model for accounting solvent effects in computational (bio-) chemistry. In the present article, we derive the analytical forces using the domain-decomposition-based LPB-method with a van-der Waals or solvent-accessible surface. We present an efficient strategy to compute the forces and its implementation, allowing linear scaling of the method with respect to the number of atoms using the fast multipole method. Numerical tests illustrate the accuracy of the computation of the analytical forces and compare the efficiency with other available methods.

Authors 5

1. Abhinav Jha

   University of Stuttgart

   Affiliation as printed

   Institute of Applied Analysis and Numerical Simulation, Universität Stuttgart 1 , Pfaffenwaldring 57, 70569 Stuttgart, Germany

2. Michele Nottoli

   University of Stuttgart

   Affiliation as printed

   Institute of Applied Analysis and Numerical Simulation, Universität Stuttgart 1 , Pfaffenwaldring 57, 70569 Stuttgart, Germany

3. Aleksandr Mikhalev Aachen Applied and Computational Mathematics

   RWTH Aachen University

   Affiliation as printed

   Applied and Computational Mathematics, RWTH Aachen University 2 , Schinkelstraße 2, 52062 Aachen, Germany

4. Chaoyu Quan

   Southern University of Science and Technology

   Affiliation as printed

   Shenzhen International Center for Mathematics , Southern University of Science and Technology 3 , Shenzhen, China

5. Benjamin Stamm

   University of Stuttgart

   Affiliation as printed

   Institute of Applied Analysis and Numerical Simulation, Universität Stuttgart 1 , Pfaffenwaldring 57, 70569 Stuttgart, Germany