A piecewise lookup table for calculating nonbonded pairwise atomic interactions.
A critical challenge for molecular dynamics simulations of chemical or biological systems is to improve the calculation efficiency while retaining sufficient accuracy. The main bottleneck in improving the efficiency is the evaluation of nonbonded pairwise interactions. We propose a new piecewise lookup table method for rapid and accurate calculation of interatomic nonbonded pairwise interactions. The piecewise lookup table allows nonuniform assignment of table nodes according to the slope of the potential function and the pair interaction distribution. The proposed method assigns the nodes more reasonably than in general lookup tables, and thus improves the accuracy while requiring fewer nodes. To obtain the same level of accuracy, our piecewise lookup table accelerates the calculation via the efficient usage of cache memory. This new method is straightforward to implement and should be broadly applicable. Graphical Abstract Illustration of piecewise lookup table method.
Key Laboratory of Thermo-Fluid Science and Engineering, Ministry of Education, School of Energy and Power Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China.
Jinping
J
Luo
Key Laboratory of Thermo-Fluid Science and Engineering, Ministry of Education, School of Energy and Power Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China. ljliu@mail.xjtu.edu.cn.
Lijun
http://orcid.org/0000-0002-6212-3036
L
Liu
Key Laboratory of Thermo-Fluid Science and Engineering, Ministry of Education, School of Energy and Power Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China.
Peng
P
Su
Key Laboratory of Thermo-Fluid Science and Engineering, Ministry of Education, School of Energy and Power Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China.
Pengbo
P
Duan
Key Laboratory of Thermo-Fluid Science and Engineering, Ministry of Education, School of Energy and Power Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China.
Daihui
D
Lu
Computer simulation; Linear lookup table; Molecular dynamics; Nonbonded pairwise interactions; Piecewise lookup table