Premium
Efficient calculations of coulombic interactions in biomolecular simulations with periodic boundary conditions
Author(s) -
Shimada Jiro,
Kaneko Hiroki,
Takada Toshikazu
Publication year - 1993
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.540140712
Subject(s) - truncation (statistics) , multipole expansion , particle (ecology) , periodic boundary conditions , computer science , boundary value problem , particle system , electrostatics , statistical physics , algorithm , computational physics , physics , chemistry , quantum mechanics , machine learning , geology , oceanography , operating system
To make improved treatments of electrostatic interactions in biomacromolecular simulations, two possibilities are considered. The first is the famous particle–particle and particle–mesh (PPPM) method developed by Hockney and Eastwood, and the second is a new one developed here in their spirit but by the use of the multipole expansion technique suggested by Ladd. It is then numerically found that the new PPPM method gives more accurate results for a two‐particle system at small separation of particles. Preliminary numerical examination of the various computational methods for a single configuration of a model BPTI–water system containing about 24,000 particles indicates that both of the PPPM methods give far more accurate values with reasonable computational cost than do the conventional truncation methods. It is concluded the two PPPM methods are nearly comparable in overall performance for the many‐particle systems, although the first method has the drawback that the accuracy in the total electrostatic energy is not high for configurations of charged particles randomly generated. © 1993 John Wiley & Sons, Inc.