Paper Citing NAMD - Abstract
Luo, Jinping; Liu, Lijun; Su, Peng; Duan, Pengbo; Lu, Daihui
A piecewise lookup table for calculating nonbonded pairwise atomic interactions
JOURNAL OF MOLECULAR MODELING, 21 Art. No. 288, NOV 2015
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.
