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

RWTH Publications (RWTH Aachen)

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 of the domain-decomposition-based ddLPB-method with vdW or SAS 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 (FMM). Numerical tests illustrates the accuracy of the computation of the analytical forces and compares efficiency with other available methods.

Authors 5

1. Abhinav Jha

   University of Stuttgart

   Affiliation as printed

   Universität Stuttgart , Institute of Applied Analysis and Numerical Simulation , Pffafenwaldring 57 , 70569 , Stuttgart , Ger - many ,

2. Michele Nottoli

   University of Stuttgart

   Affiliation as printed

   Universität Stuttgart , Institute of Applied Analysis and Numerical Simulation , Pffafenwaldring 57 , 70569 , Stuttgart , Ger - many ,

3. Aleksandr Mikhalev Aachen

   RWTH Aachen University

   Affiliation as printed

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

4. Chaoyu Quan

   Southern University of Science and Technology

   Affiliation as printed

   SUSTech International Center for Mathematics , and Guangdong Provincial Key Laboratory of Computational Science and Material Design , Southern University of Science and Technology , Shenzhen , China,

5. Benjamin Stamm

   University of Stuttgart

   Affiliation as printed

   Universität Stuttgart , Institute of Applied Analysis and Numerical Simulation , Pffafenwaldring 57 , 70569 , Stuttgart , Ger - many ,