Fast Decorrelating Monte Carlo Moves for Efficient Path Sampling

Nearly 20 years ago, transition path sampling (TPS) emerged as an alternative method to free energy based approaches for the study of rare events such as nucleation, protein folding, chemical reactions, and phase transitions. TPS effectively performs Monte Carlo simulations with relatively short molecular dynamics trajectories, with the advantage of not having to alter the actual potential energy surface nor the underlying physical dynamics. Although the TPS approach also introduced a methodology to compute reaction rates, this approach was for a long time considered theoretically attractive, providing the exact same results as extensively long molecular dynamics simulations, but still expensive for most relevant applications. With the increase of computer power and improvements in the algorithmic methodology, quantitative path sampling is finding applications in more and more areas of research. In particular, the transition interface sampling (TIS) and the replica exchange TIS (RETIS) algorithms have, in turn, improved the efficiency of quantitative path sampling significantly, while maintaining the exact nature of the approach. Also, open-source software packages are making these methods, for which implementation is not straightforward, now available for a wider group of users. In addition, a blooming development takes place regarding both applications and algorithmic refinements. Therefore, it is timely to explore the wide panorama of the new developments in this field. This is the aim of this article, which focuses on the most efficient exact path sampling approach, RETIS, as well as its recent applications, extensions, and variations. Published by AIP Publishing.

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“…An approach to decorrelate the paths much faster was suggested in Ref. 61 via the so-called stone skipping and web-throwing moves (Fig. 11).…”

Section: A New Shooting Movesmentioning

confidence: 99%

“…The new shooting moves showed a factor 12 improvement compared to standard shooting in a study for DNA denaturation. 61 …”

Section: A New Shooting Movesmentioning

confidence: 99%

Foundations and latest advances in replica exchange transition interface sampling

Cabriolu

Refsnes

Bolhuis

et al. 2017

The Journal of Chemical Physics

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“…After modifying the velocities of this phase point (e.g. by randomly drawing new velocities from a Maxwellian distribution), a new trajectory is generated and accepted or rejected according to a detailed balance 20,37 condition. This condition ensures unbiased sampling.…”

Section: Replica Exchange Transition Interface Samplingmentioning

confidence: 99%

“…In the first case, the internal MD engine has been used to simulate a particle moving in a 2D potential surface. 20 The second and third cases are examples of using CP2K 21 for simulating hydrogen splitting and proton transfer in water respectively. Finally, we show an example of using GROMACS 22 for studying the diffusion of a methane molecule into a water hydrate.…”

Section: Pyretis Examplesmentioning

confidence: 99%

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

2017

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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.

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PyRETIS 2: An improbability drive for rare events

et al. 2019

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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.

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Fast Decorrelating Monte Carlo Moves for Efficient Path Sampling

Cited by 25 publications

References 24 publications

Foundations and latest advances in replica exchange transition interface sampling

Foundations and latest advances in replica exchange transition interface sampling

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

PyRETIS 2: An improbability drive for rare events

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