École Nationale Supérieure de
Techniques Avancées

Abstract

The goal of molecular dynamics is to simulate the trajectory of microscopic molecu- lar systems, which implies a time discretization with time-steps of order 1 femtosecond (10−15 s). Following the implementation of a multi time-step algorithm in the Tinker software (separation of quick forces calculated at each time-step and slow forces calcu- lated every n time-steps), this paper explains the implementation of a new algorithm using velocity jump processes. The idea is to no longer calculate the slow forces with a fixed time-step, but the calculate them with a certain probability at each time-step. This probability is chosen specifically to remove the systematic bias caused by fixing the time-step in multi time-step algorithms.