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

5 years ago

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

Enrico Riccardi, Anders Lervik, Titus S. van Erp

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, for example, 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. © 2017 Wiley Periodicals, Inc. PyRETIS is a Python-based code to sample rare events in path space. It can handle different types of dynamics and it can be easily interfaced with different software at different resolution levels. Proton transfer between water molecules and biomolecule-DNA binding are just two examples of the transitions that PyRETIS can describe quantitatively without the implementation of any bias.

Publisher URL: http://onlinelibrary.wiley.com/resolve/doi

DOI: 10.1002/jcc.24900