On periodic boundary conditions for chain molecule in off lattice model

E. M. Pestryaev

Matematičeskoe modelirovanie, Tome 16 (2004) no. 2, pp. 102-110.

Résumé

Periodic boundary conditions algorithm for chain molecule in off lattice molecular dynamics has been developed. The chain length can be essentially more than any size of modeled volume. The algorithm permits to save system puck coefficient by replacement of chain part out of the modeled volume by virtual particles and to simulate chain large-scale motions. The algorithm has been completed by virtual displacement method to observe chain mass center displacement exceeding chain characteristic size and modeled system size. The virtual displacement method is based on the application of kinematical quantities, which do not change under realization of periodic boundary conditions unlike the displacement itself, which cannot exceed the modeled volume sizes.

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