# 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 buildβ¦Β

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## 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.

- PhysicsThe journal of physical chemistry. B
- 2009

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.

- Computer ScienceFaraday discussions
- 2016

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

- Computer ScienceEntropy
- 2014

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.

- PhysicsJournal of chemical theory and computation
- 2011

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

- PhysicsPhilosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences
- 2014

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.

- PhysicsThe journal of physical chemistry. A
- 2018

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

- Chemistry
- 2000

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 aβ¦

### The Modern Temperature-Accelerated Dynamics Approach.

- PhysicsAnnual review of chemical and biomolecular engineering
- 2016

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.

- PhysicsThe Journal of chemical physics
- 2006

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

- Physics
- 1997

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 theβ¦