Treecode algorithm for pairwise electrostatic interactions with solvent-solute polarization.
An O(N log N) treecode algorithm is presented for computing pairwise interactions of electrostatic free energy for reaction potentials with polarization effects due to the macroscopic solvent. A multipole expansion for a cluster is used to account for particles inside the cluster, where a spatial difference is applied to obtain the expansion coefficients of the polarization function. Numerical tests are performed to illustrate the accuracy and efficiency of the approach. The algorithm is significant in speeding up generalized Born methods for biomolecular simulations under the framework of macroscopically treating solvents.
Xu
Zhenli
Z
Department of Mathematics, Shanghai Jiao Tong University, Shanghai 200240, China and Department of Mathematics and Statistics, University of North Carolina, Charlotte, North Carolina 28223, USA. xuzl@ustc.edu
D000465:Algorithms; D003198:Computer Simulation; D056004:Molecular Dynamics Simulation; D012997:Solvents / Q000737:chemistry*; D055672:Static Electricity; D013816:Thermodynamics; D013997:Time Factors
D012997:Solvents