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Standard molecular dynamics simulation necessarily uses a very small time step, on the order of femtoseconds, to capture the dynamics of the modeled atoms. However, this limits the total duration of a simulation to tens of nanoseconds, a time span too short to observe many physical phenomena. There are methods available to address this issue for modeling of so-called infrequent event systems. An infrequent event system is one for which time can be separated into the short time scale of a “transition” event and the long time scale of the periods between transition events. Accelerated molecular dynamics methods take advantage of this behavior to lengthen simulations by increasing the probability that infrequent events will occur.
This presentation will include an introduction to several accelerated molecular dynamics methods. However, particular focus will be given to parallel replica (ParRep) dynamics in which atomistic simulations are run parallel in time to extend their total duration. The ParRep method is based on the assumptions that the system being modeled advances to new configurations via infrequent events and that there are well-defined instantaneous rate constants for these events that are independent of the driving rate. The method distributes the simulation time across multiple processors and therefore adequately samples the various possible state-to-state pathways accessible to the system, as would a standard, single-processor molecular dynamics run for a very long time.
One example of an infrequent event system is the stick-slip behavior observed during atomic-scale friction. In this beautiful yet poorly understood phenomenon, sliding does not occur stably. Rather, the two surfaces stick together and lateral strain builds up. At some critical point the surfaces slide (usually, but not always, by one atomic lattice site), then they lock together again. Stick-slip friction is ideally suited for accelerated molecular dynamics since the time between slip events is typically much longer than the duration of the slip itself. An overview of how parallel replica dynamics can be applied to model atomic-scale stick-slip friction as well as some results obtained using that method will be presented.
Researchers should cite this work as follows:
Ashlie Martini (2010), "Addressing Molecular Dynamics Time-scale Issues to Study Atomic-scale Friction," https://nanohub.org/resources/9856.
3102 Lawson Hall, Purdue University, West Lafayette, IN