The Flexible Rare Event Sampling Harness System (FRESHS)

Kratzer, Kai; Berryman, Joshua T.; Taudt, Aaron; Zeman, Johannes; Arnold, Axel

doi:10.1016/j.cpc.2014.03.013

Cited by 18 publications

(19 citation statements)

References 44 publications

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“…These methods apply bias potentials to reduce potential energy barriers. Another group includes the Temperature‐Accelerated Dynamics (TAD) method, which adds kinetic energy distributed randomly over all configurations by an increase of temperature, or the Forward Flux Sampling (FFS) method that adds kinetic energy only to configurations specified by an order parameter. Another possibility to increase the observation probability of infrequent events, such as reaction events, is the exploitation of parallelization as in the parallel replica method .…”

Section: Introductionmentioning

confidence: 99%

Exploring the Chemistry of Low‐Temperature Ignition by Pressure‐Accelerated Dynamics

et al. 2020

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Reaction models that accurately describe the complex reaction processes of ignition are key for the development of novel engine-and fuel concepts. Since reactive molecular dynamics can be used to discover reaction networks in a largely automated fashion, this method has the potential to drastically reduce the real time effort necessary for the development of reaction models. With standard reactive molecular dynamics, the simulation of low-temperature reaction processes is hindered by the small accessible time scales of only a few nanoseconds. In this work, we propose the pressure-accelerated dynamics method to overcome the time scales obstacle through exploitation of Le Chatelier's principle. For the example of pentane low-temperature ignition, we show that with pressure-accelerated dynamics, the ReaxFF reactive force field, and the ChemTraYzer not only the known key low-temperature igniton pathways can be found, but also reactions that are not yet included in reaction models.

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Section: Introductionmentioning

confidence: 99%

Exploring the Chemistry of Low‐Temperature Ignition by Pressure‐Accelerated Dynamics

et al. 2020

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“…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. [109] There are also many software packages, such as PLUMED, [110] for biased rare event methods.…”

Section: Overviewmentioning

confidence: 99%

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

Bolhuis

Swenson

2021

Advcd Theory and Sims

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The development of enhanced sampling methods to investigate rare but important events has always been a focal point in the molecular simulation field. Such methods often rely on prior knowledge of the reaction coordinate. However, the search for this reaction coordinate is at the heart of the rare event problem. Transition path sampling (TPS) circumvents this problem by generating an ensemble of dynamical trajectories undergoing the activated event. The reaction coordinate is extracted from the resulting path ensemble using variants of machine learning, making it an output of the method instead of an input. Over the last 20 years, since its inception, many extensions of TPS have been developed. Perhaps surprisingly, large‐scale TPS simulations on complex molecular systems have become possible only recently. Other important developments include the transition interface sampling (TIS) methodology to compute rate constants, the application to multiple states, and adaptive path sampling. The development of OpenPathSampling and PyRETIS has enabled easy and flexible use and implementation of these and other novel path sampling algorithms. In this progress report, a brief overview of recent developments, novel algorithms, and software is given. In addition, several application areas are discussed, and a future outlook for the next decade is given.

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“…As noted in Section II, several highly scalable packages are currently available, including WESTPA, AWE-WQ and FRESHS, which have demonstrated inter-operability with a variety of dynamics engines [*50,52,69]. A competitive software ecosystem with additional robust packages should be a boon to the field.…”

Section: Challengesmentioning

confidence: 99%

Path-sampling strategies for simulating rare events in biomolecular systems

Chong

Saglam

Zuckerman

2017

Current Opinion in Structural Biology

105

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Despite more than three decades of effort with molecular dynamics simulations, long-timescale (ms and beyond) biologically relevant phenomena remain out of reach in most systems of interest. This is largely because important transitions, such as conformational changes and (un)binding events, tend to be rare for conventional simulations (< 10 µs). That is, conventional simulations will predominantly dwell in metastable states instead of making large transitions in complex biomolecular energy landscapes. In contrast, path sampling approaches focus computing effort specifically on transitions of interest. Such approaches have been in use for nearly 20 years in biomolecular systems and enabled the generation of pathways and calculation of rate constants for ms processes, including large protein conformational changes, protein folding, and protein (un)binding.

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The Flexible Rare Event Sampling Harness System (FRESHS)

Cited by 18 publications

References 44 publications

Exploring the Chemistry of Low‐Temperature Ignition by Pressure‐Accelerated Dynamics

Exploring the Chemistry of Low‐Temperature Ignition by Pressure‐Accelerated Dynamics

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

Path-sampling strategies for simulating rare events in biomolecular systems

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