Parallel Algorithm for Molecular Dynamics Integration

A new parallel implementation of a long-range interaction problem on the ring topology for a MIMD computer system is presented. The algorithm was applied for the implementation of a forces integrator in the molecular dynamics. The complexity estimation is made and also measured time results are given. It is shown that for each number of particles N there exists an optimal number of processors p. Time complexity O(N 2 ) of a sequential algorithm is reduced to O(N 2 =p) with the proposed parallel implementation. The time requirement for the optimal sequential algorithm is proportional to N 2 =2 and the time requirement for the proposed parallel algorithm is proportional to N 2 =(2p). 1 Keywords. Parallel algorithm; transputer ring topology; long-range interactions; molecular dynamics; complexity estimation. -------------------------------------------- Author to whom all correspondence should be addressed: Fax: +38 61 161 029, E-mail: [email protected] 1 In Parallel Compu..