Conformational Ensembles from Experimental Data and Computer Simulations

68 / 161

Conformational Ensembles from Experimental Data
and Computer Simulations Poster Abstracts
64
31-POS Board 31
Non-Ewald Method for Accurately and Efficiently Calculating Electrostatic Interactions in
Molecular Simulations
Ikuo Fukuda1, Narutoshi Kamiya2, Kota Kasahara3, Han Wang4 , Shun Sakuraba5, Haruki
Nakamura1 .
1Osaka University, Suita, Osaka, Japan, 2University of Hyogo, Kobe, Japan, 3Ritsumeikan
University, Kusatsu, Japan, 4Institute of Applied Physics and Computational Mathematics,
Beijing, China, 5The University of Tokyo, Tokyo, Japan.
A larger system and longer time steps are necessary to conduct a realistic molecular simulation,
but they are hardly realized in current computational environments. The most time-consuming
part of the simulation is the calculation of long-range interactions of particles. In particular,
appropriate treatment of the electrostatic interaction is critical, since the simple truncation cannot
be used due to the slow decay of the Coulombic function. Thus, there is strong demand to
calculate the electrostatic interactions with high accuracy and low computational cost.
For this purpose, we have developed the Zero-multipole summation method (ZMM) [1]. In this
method, the periodic boundary condition, which can potentially cause artifacts in particular for
heterogeneous systems, is not necessary, and the Fourier-part evaluation, which is typically the
bottleneck for high performance computation, is not needed, in contrast to conventional Ewald-
based methods. Instead, a suitably defined simple pairwise function, which differs from the
original Coulombic function, is used with a cutoff scheme. The underling physical idea is simple
that certain electrostatic neutrality is attained in a biological or condensed matter system [2].
This idea is realized by a mathematical foundation to generate a new pairwise function. The
accuracy and efficiency of the ZMM has been validated in fundamental systems as well as
heterogeneous biomolecular systems, including DNA and protein. In the presentation, we will
provide the theory and numerical results on the ZMM, and discuss how the treatment of the
electrostatic calculations seriously affects simulation results.
[1] I. Fukuda, J. Chem. Phys. 139, 174107 (2013); I. Fukuda et al., ibid. 140,194307 (2014); H.
Wang et al., ibid. 144, 114503 (2016); K. Kasahara, et al., Biophys. Physicobiol., 13, 209 (2016).
[2] I. Fukuda and H. Nakamura, Biophys. Rev. 4, 161 (2012).