PyRETIS: A well-done, medium-sized python library for rare events

Abstract

Transition Path Sampling techniques are becoming common approaches in the study of rare events at the molecular scale. More efficient methods, such as transition interface sampling (TIS) and replica exchange transition interface sampling (RETIS), allow the investigation of rare events, e.g. chemical reactions and structural/morphological transitions, in a reasonable computational time. Here, we present pyretis, a Python library for performing TIS and RETIS simulations. pyretis directs molecular dynamics (MD) simulations in order to sample rare events with unbiased dynamics. pyretis is designed to be easily interfaced with any molecular simulation package and in the present release, it has been interfaced with GROMACS and CP2K, for classical and ab initio MD simulations, respectively.