TY - JOUR
T1 - A fast and accurate computational method for the linear-combination-based isotropic periodic sum
AU - Takahashi, Kazuaki Z.
AU - Nozawa, Takuma
AU - Yasuoka, Kenji
N1 - Funding Information:
We sincerely thank Dr. Ryuji Sakamaki of X-Ability Co., Ltd. for his great effort in implementing LIPS/FFT within CHARMM (version c40b2). KZT was supported in part by the Japan Society for the Promotion of Science (JSPS) Grants-in-Aid for Scientific Research (KAKENHI) Grant Number 16H06071. TN was supported in part by Grant-in-Aid for JSPS Fellows, and Ministry of Education, Culture, Sports, Science and Technology (MEXT) Grant-in-Aid for the Program for Leading Graduate Schools.
Publisher Copyright:
© 2018, The Author(s).
PY - 2018/12/1
Y1 - 2018/12/1
N2 - An isotropic periodic sum (IPS) is a powerful technique to reasonably calculate intermolecular interactions for wide range of molecular systems under periodic boundary conditions. A linear-combination-based IPS (LIPS) has been developed to attain computational accuracy close to an exact lattice sum, such as the Ewald sum. The algorithm of the original LIPS method has a high computational cost because it needs long-range interaction calculations in real space. This becomes a performance bottleneck for long-time molecular simulations. In this work, the combination of an LIPS and fast Fourier transform (FFT) was developed, and evaluated on homogeneous and heterogeneous molecular systems. This combinational approach of LIPS/FFT attained computational efficiency close to that of a smooth particle mesh Ewald while maintaining the same high accuracy as the original LIPS. We concluded that LIPS/FFT has great potential to extend the capability of IPS techniques for the fast and accurate computation of many types of molecular systems.
AB - An isotropic periodic sum (IPS) is a powerful technique to reasonably calculate intermolecular interactions for wide range of molecular systems under periodic boundary conditions. A linear-combination-based IPS (LIPS) has been developed to attain computational accuracy close to an exact lattice sum, such as the Ewald sum. The algorithm of the original LIPS method has a high computational cost because it needs long-range interaction calculations in real space. This becomes a performance bottleneck for long-time molecular simulations. In this work, the combination of an LIPS and fast Fourier transform (FFT) was developed, and evaluated on homogeneous and heterogeneous molecular systems. This combinational approach of LIPS/FFT attained computational efficiency close to that of a smooth particle mesh Ewald while maintaining the same high accuracy as the original LIPS. We concluded that LIPS/FFT has great potential to extend the capability of IPS techniques for the fast and accurate computation of many types of molecular systems.
UR - http://www.scopus.com/inward/record.url?scp=85051255036&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85051255036&partnerID=8YFLogxK
U2 - 10.1038/s41598-018-30364-2
DO - 10.1038/s41598-018-30364-2
M3 - Article
C2 - 30089878
AN - SCOPUS:85051255036
SN - 2045-2322
VL - 8
JO - Scientific reports
JF - Scientific reports
IS - 1
M1 - 11880
ER -