The algorithm is based on a grid search and on partitioning of the atoms into boxes rather than on calculations of distances. The effort associated with the generation of the box list grows only linearly with the number of atoms. The algorithm is particularly advantageous for solvated systems. Test
The neighbor list algorithm for a parallelepiped box in molecular dynamics simulations
β Scribed by Cui, ZhiWei ;Sun, Yi ;Qu, JianMin
- Book ID
- 107368899
- Publisher
- Elsevier
- Year
- 2009
- Tongue
- English
- Weight
- 722 KB
- Volume
- 54
- Category
- Article
- ISSN
- 2095-9273
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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 vect