Adaptively Accelerating Reactive Molecular Dynamics Using Boxed Molecular Dynamics in Energy Space.

@article{Shannon2018AdaptivelyAR,
  title={Adaptively Accelerating Reactive Molecular Dynamics Using Boxed Molecular Dynamics in Energy Space.},
  author={Robin J. Shannon and Silvia Amabilino and Michael B. O'Connor and Dmitrii V Shalishilin and David R. Glowacki},
  journal={Journal of chemical theory and computation},
  year={2018},
  volume={14 9},
  pages={
          4541-4552
        }
}
The problem of observing rare events is pervasive among the molecular dynamics community and an array of different types of methods are commonly used to accelerate these long time scale processes. Typically, rare event acceleration methods require an a priori specification of the event to be accelerated. In recent work, we have demonstrated the application of boxed molecular dynamics to energy space, as a way to accelerate rare events in the stochastic chemical master equation. Here we build… 

Accelerated sampling methods for high dimensional molecular systems

Improvements to simulation methods for accessing rare events are presented and a virtual reality framework for interactive molecular dynamics (iMD-VR) is presented as a strategy for the rapid identification of pathways and collective variables that can be used with existing accelerated molecular dynamics methods.

ChemDyME: Kinetically Steered, Automated Mechanism Generation through Combined Molecular Dynamics and Master Equation Calculations.

This work presents a new approach to automated mechanism generation which couples molecular dynamics and statistical rate theory to automatically find kinetically important reactions and then solve the time evolution of the species in the evolving network.

Automatic Approach to Explore the Multireaction Mechanism for Medium-Sized Bimolecular Reactions via Collision Dynamics Simulations and Transition State Searches.

An automatic approach to explore multireaction mechanism for medium-sized bimolecular reactions via collision dynamics simulations and transition state searches is explored.

Enhancing Automated Reaction Discovery with Boxed Molecular Dynamics in Energy Space

The rare event acceleration method BXDE is interfaced in the present work with the automated reaction discovery method AutoMeKin. To test the efficiency of the combined AutoMeKin-BXDE procedure, the

Expansive Quantum Mechanical Exploration of Chemical Reaction Paths.

Explorative approaches are likely to replace the current state of the art in computational chemistry, because they reduce the human effort to be invested in reaction path elucidations, they are less prone to errors and bias-free, and they cover more extensive regions of the relevant configuration space.

Efficient Reaction Space Exploration with ChemTraYzer-TAD

The development of a reaction model is often a time-consuming process, especially if unknown reactions have to be found and quantified. To alleviate the reaction modeling process, automated

A Trajectory-Based Method to Explore Reaction Mechanisms

The tsscds method discovers chemical reaction mechanisms with minimal human intervention using accelerated molecular dynamics, spectral graph theory, statistical rate theory and stochastic simulations to solve mechanistic/kinetics problems in different research areas.

1 A Trajectory-Based Method to Explore Reaction 2 Mechanisms 3

The tsscds method, recently developed in our group, discovers chemical reaction 11 mechanisms with minimal human intervention. It employs accelerated molecular dynamics, 12 spectral graph theory,

Interactive molecular dynamics in virtual reality from quantum chemistry to drug binding: An open-source multi-person framework.

Various efforts to extend immersive technologies to the molecular sciences are outlined, and "Narupa," a flexible, open-source, multiperson iMD-VR software framework which enables groups of researchers to simultaneously cohabit real-time simulation environments to interactively visualize and manipulate the dynamics of molecular structures with atomic-level precision is introduced.

Chemoton 2.0: Autonomous Exploration of Chemical Reaction Networks.

This work presents their approach to an open-source, extensible framework for explorations of chemical reaction mechanisms based on the first-principles of quantum mechanics, intended to facilitate reaction network explorations for diverse chemical problems with a wide range of goals.

References

SHOWING 1-10 OF 51 REFERENCES

Boxed molecular dynamics: a simple and general technique for accelerating rare event kinetics and mapping free energy in large molecular systems.

A simple, comprehensive technique for accelerating simulation of rare events and calculating free energy profiles in molecular dynamics (MD) simulations based on two related and complementary methods, which provide both thermodynamic and kinetic information along some reaction coordinate.

Adaptive free energy sampling in multidimensional collective variable space using boxed molecular dynamics.

An algorithm for adaptively generating boundaries along a free energy surface in multi-dimensional collective variable (CV) space, building on the boxed molecular dynamics (BXD) rare event algorithm.

Characterization of Rare Events in Molecular Dynamics

The optimal control approach described in detail resembles the use of Jarzynski's equality for free energy calculations, but with an optimized protocol that speeds up the sampling, while (theoretically) giving variance-free estimators of the rare events statistics.

Boxed Molecular Dynamics: Decorrelation Time Scales and the Kinetic Master Equation.

Interrelations between BXD and a recently described Markovian milestoning technique are discussed and a simple application is used to show that, despite each method producing distinct nonstatistical effects on time scales on the order of dynamical decorrelation, both yield similar long-time kinetics.

Recent applications of boxed molecular dynamics: a simple multiscale technique for atomistic simulations

Previous applications of BXD to peptide cyclization, solution phase organic reaction dynamics and desorption of ions from self-assembled monolayers (SAMs) are reviewed and preliminary results of simulations of diamond etching mechanisms and protein unfolding in atomic force microscopy experiments are reported.

A Simple "Boxed Molecular Kinetics" Approach To Accelerate Rare Events in the Stochastic Kinetic Master Equation.

This Article presents a rigorous method for accelerating stochastic approaches by several orders of magnitude, along with a method for unbiasing the accelerated results to recover the "true" value.

Accelerating rare events in ab initio molecular dynamics simulations

The ab initio mol. dynamics method developed by Car and Parrinello combines an electronic structure method based on d. functional theory (DFT) with a classical mol. dynamics scheme. This provides a

The Modern Temperature-Accelerated Dynamics Approach.

The ongoing evolution of the modern TAD method is reviewed and the latest development: speculatively parallel TAD is introduced, leveraging parallel programming techniques to enhance both the spatial and temporal scaling of the traditional approach.

Simulating rare events in equilibrium or nonequilibrium stochastic systems.

Three algorithms for calculating rate constants and sampling transition paths for rare events in simulations with stochastic dynamics, which use a series of interfaces in phase space to generate transition paths as chains of connected partial paths, in a ratchetlike manner.

Hyperdynamics: Accelerated Molecular Dynamics of Infrequent Events

I derive a general method for accelerating the molecular-dynamics (MD) simulation of infrequent events in solids. A bias potential ({Delta}V{sub b}) raises the energy in regions other than the
...