PyRETIS 2: An improbability drive for rare events

Abstract

The algorithmic development in the field of path sampling has made tremendous progress in recent years. Although the original transition path sampling method was mostly used as a qualitative tool to sample reaction paths, the more recent family of interface‐based path sampling methods has paved the way for more quantitative rate calculation studies. Of the exact methods, the replica exchange transition interface sampling (RETIS) method is the most efficient, but rather difficult to implement. This has been the main motivation to develop the open‐source Python‐based computer library PyRETIS that was released in 2017. PyRETIS is designed to be easily interfaced with any molecular dynamics (MD) package using either classical or ab initio MD. In this study, we report on the principles and the software enhancements that are now included in PyRETIS 2, as well as the recent developments on the user interface, improvements of the efficiency via the implementation of new shooting moves, easier initialization procedures, analysis methods, and supported interfaced software. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.

Transition Path Sampling as Markov Chain Monte Carlo of Trajectories: Recent Algorithms, Software, Applications, and Future Outlook

“…PyRETIS [ 105,106 ] and OpenPathSampling [ 103,104,111 ] are both Python packages, and, in broad strokes, are very similar. Both use other tools, such as OpenMM [ 112 ] and Gromacs [ 113 ] for high performance MD.…”

“…The fact that all TIS methods depend on this flexible-length approach, combined with the rapid creation of new algorithms as described in previous sections, has led to the development of software packages entirely focused on path sampling. The primary packages currently in active development in this field are OpenPathSampling [103,104] and PyRETIS, [105,106] both of which are Python codes that can interface with multiple underlying MD engines. Other software packages for trajectory-based rare event methods include WESTPA, [107] FRESHS, [108] and SSAGES.…”

Exploring the effects of approach velocity on depletion force and coalescence in oil-in-water emulsions

“…Additionally, the combined efforts of experimental measurements detailed in this paper and simulations will be important for further progress in the understanding of these emulsions. Ongoing experimental studies are therefore in our group complemented by the use of rare event simulations using the PyRETIS 62,63 and PyVisA 64 packages to aid in understanding the dynamics of thin lm breakage.…”

Path sampling for atmospheric reactions: formic acid catalysed conversion of SO3 + H2O to H2SO4

“…All initial paths were generated by the PyRETIS kick method , whereby a path is constructed starting from the initial configuration by altering velocities at each step and only accepting the step if it increases the value of s(r). In some cases, after a short equilibration run simulations were restarted by using the PyRETIS load function (Riccardi et al, 2019a) to start from the final path accepted in the first simulation. In general, initial paths generated by kick (an approach based on a combination of Monte Carlo and BO-MD) can require many cycles to find physically realistic reaction paths; in this particular study, the initial paths agree closely with the real reaction pathways found using RETIS.…”