Molecular Dynamics Simulation Methods

A major difficulty in MD-simulation methods is the complexity of the long range force evaluation in each time step. To cope with this problem, various multiscale type methods had been developed, i.e. treecodes, multipole approaches or multigrid techniques, which reduces the O(N^2) complexity of the naive approach to O(N log N) or even O(N).

A further reduction on execution time is possible by parallelization. Here, however - especially for adaptive tree-type methods - the implementation is quite difficult and cumbersome.

Our approach, which we have now implemented, is a variant of the adaptive Barnes-Hut/Multipole method (see also: J.K. Salmon & M.S. Warren, Int. J. Supercomp. App. , Vol.8.2). We use a hash-technique for dealing with the adaptivity of the method and parallelize with space-filling curves by assigning segments of the increasingly ordered hashtable-key list to each processor.

Altogether this results in an efficient long-range (Coulomb, van der Waals) force evaluation without potential cut-off and a simple incorporation of short-range forces.

We have applied this approach to the simulation of a NaCl-melting process and use it also in the examination of the dynamical behaviour of the Bovine-Pancreatic-Trypsin-Inhibitor (BPTI).

Bovine-Pancreatic-Trypsin-Inhibitor:

NaCl-Melting:

Startconfig.: uniform grid, 1014 Na, 1014 Cl ions, Maxwell-Boltzmann velocity distribution at 1800 K. Particle configuration for NaCl at time 0.47, 0.94 and 1.41 (time-unit 1.03e-15 sec.).

Thomas Gerstner,