2015
DOI: 10.1063/1.4935180
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Nonparametric variational optimization of reaction coordinates

Abstract: State of the art realistic simulations of complex atomic processes commonly produce trajectories of large size, making the development of automated analysis tools very important. A popular approach aimed at extracting dynamical information consists of projecting these trajectories into optimally selected reaction coordinates or collective variables. For equilibrium dynamics between any two boundary states, the committor function also known as the folding probability in protein folding studies is often consider… Show more

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Cited by 27 publications
(60 citation statements)
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“…Indeed the algorithm proposed in the present work is similar to these previous studies. It is also similar in spirit to references [25,26]. However, there are conceptual and algorithmic differences between these investigations, which are discussed later in the article.…”
Section: Methodssupporting
confidence: 55%
See 1 more Smart Citation
“…Indeed the algorithm proposed in the present work is similar to these previous studies. It is also similar in spirit to references [25,26]. However, there are conceptual and algorithmic differences between these investigations, which are discussed later in the article.…”
Section: Methodssupporting
confidence: 55%
“…However, it is limited to a small number of degrees of freedom since the complexity of the solution increases exponentially with the dimensionality of the system. Studies of committors [26,2830] in systems with high dimension use estimates based on trajectory sampling. Trajectory-based formulation makes it possible to use arbitrary dynamics and not limit the choice to overdamped Langevin.…”
Section: Methodsmentioning
confidence: 99%
“…In the protein folding example, we see that deflation can obscure a long-timescale process from a kinetic model in order to facilitate further analysis that is desired to be independent of that process. In MD simulations, the dominant processes may not be the same as the processes of interest due to low sampling or force field artifacts 8,9 . Thus, deflation presents a systematic way of removing the effects of these undesired modes on model building.…”
Section: Discussionmentioning
confidence: 99%
“…Integrating Eq. over r one obtains true false∫ 0 1 Z C , 1 (), r Δ t d r = 1 false/ 2 true false∑ i r Δ t + i Δ t r i Δ t 2 = 1 false/ 2 〈〉 Δ r 2 () Δ t () N Δ t 0 false/ Δ t or 〈〉 Δ r 2 () Δ t = 2 Δ t false/ () N Δ t 0 〈〉 Z C , 1 () Δ t which means that if 〈 Z C ,1 (Δ t )〉 is constant (increases with Δ t , decreases with Δ t ) the equilibrium mean squared displacement grows linearly (faster than linear, slower than linear) with time . For the committor one specifically obtains 〈Δ q 2 (Δ t )〉 = 2 ΔtJ AB .…”
Section: The Committor As An Optimal Rcmentioning
confidence: 99%
“…Then, one numerically optimizes the weights w ij or the cutoff distances r i j 0 for contacts by optimizing a particular functional, so that in the end, the putative RC accurately approximates the committor. The following optimization functionals have been suggested: the probability of being on a transition path, the likelihood functional, the cut profiles, and the total squared displacement (TSD) …”
Section: Validation and Determination Of Optimal Rcsmentioning
confidence: 99%