Paper Citing NAMD - Abstract
Jung, Jaewoon; Mori, Takaharu; Sugita, Yuji
Efficient Lookup Table Using a Linear Function of Inverse Distance Squared
JOURNAL OF COMPUTATIONAL CHEMISTRY, 34:2412-2420, OCT 30 2013
The major bottleneck in molecular dynamics (MD) simulations of biomolecules exist in the calculation of pairwise nonbonded interactions like Lennard-Jones and long-range electrostatic interactions. Particle-mesh Ewald (PME) method is able to evaluate long-range electrostatic interactions accurately and quickly during MD simulation. However, the evaluation of energy and gradient includes time-consuming inverse square roots and complementary error functions. To avoid such time-consuming operations while keeping accuracy, we propose a new lookup table for short-range interaction in PME by defining energy and gradient as a linear function of inverse distance squared. In our lookup table approach, densities of table points are inversely proportional to squared pair distances, enabling accurate evaluation of energy and gradient at small pair distances. Regardless of the inverse operation here, the new lookup table scheme allows fast pairwise nonbonded calculations owing to efficient usage of cache memory. (c) 2013 Wiley Periodicals, Inc.
