This paper addresses the automatic update of the Verlet neighbor list for use in molecular dynamics simulations. We investigate the effects of density, temperature, time step, system size and molecular geometry upon the optimum neighbor list radius, update frequency, and timing of an explicitly vectorized algorithm. We find agreement between theoretical predictions (according to which the optimum neighbor list radius increases with sample size, temperature and time step, and decreases with density, elongation and number of sites, whereas the speed-up due to the use of neighbor lists increases linearly with sample size and decreases with density) and simulation results.
All Science Journal Classification (ASJC) codes
- Hardware and Architecture
- Physics and Astronomy(all)