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Zhidk. krist. ikh prakt. ispol'z. = Liq. Cryst. and their Appl., 2014, 14 (1), 87—93.
Algorithms For Calculation of van der Waals Interactions on Graphics Processing Units For Molecular Dynamics Simulation. Evaluation of Their Effectiveness
D. O. Moskvin, V. V. Sotsky, N. V. Usol'tseva
Author affiliations Nanomaterials Research Institute, Ivanovo State University, Ermak str., 39, 153025 Ivanovo, Russia. E-mail: Moskvin1987@mail.ru
Abstract The problem of transfer of the Verlet neighbour lists algorithm and the linked lists algorithm (cell method) for calculation of van der Waals interactions to graphics processing units for molecular dynamics simulation is examined. The effectiveness of the adapted algorithms is evaluated. It is shown that the Verlet list and linked list algorithms adapted for graphics processing units are more effective (in 39.5 and 10 times, correspondingly) than the algorithms working on four central processing units (distribution of calculations is performed using the OpenMP library).
Keywords: van der Waals interactions, molecular dynamics, Verlet neighbour lists, linked lists, graphics processing units.