Nonlinear reaction coordinate analysis in the reweighted path ensemble

Abstract

Nonlinear reaction coordinate analysis in the reweighted path ensembleLechner, W.; Rogal, J.G.; Juraszek, J.; Ensing, B.; Bolhuis, P.G. General rightsIt is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), other than for strictly personal, individual use, unless the work is under an open content license (like Creative Commons). Disclaimer/Complaints regulationsIf you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: http://uba.uva.nl/en/contact, or a letter to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. You will be contacted as soon as possible.

Role of the Prestructured Surface Cloud in Crystal Nucleation

“…[9]). This method takes the RPE [8] as the input data set, which is obtained from a replica exchange transition interface sampling simulation, followed by reweighting all configurations from all paths to their equilibrium weights wðxÞ.…”

“…and r½qðxÞ is the RC model [9]. The first sum goes over all configurations x A that are part of RPE paths that end in A weighted by wðx A Þ, the second sum accordingly over all configurations that end in B.…”

“…This leads to a parameter 2 ½0; 1 , denoting the progress along the string, which is mapped to r by a monotonic function rð Þ. Using a Monte Carlo annealing scheme, we maximize the log likelihood lnL with respect to (i) the string, (ii) the mapping function rð Þ, and (iii) a relative scaling s of the CVs [9]. We study the nucleation at moderate undercooling in the high as well as the low pressure regime of the Gaussian core model [see phase diagram in Fig.…”

“…To find such a low dimensional representation we make use of the recently developed method to extract nonlinear RCs from the reweighted path ensemble (RPE) [8,9]. This method is based on calculating the likelihood that a given representation follows an ideal committor function, which serves as a measure for the quality of the OPs and allows for a systematic evaluation of RCs without any a priori…”

“…In this study, we use a new computational technique [8,9] and new structural OPs to find optimal RCs for crystal nucleation, in terms of a low dimensional set of CVs. To find such a low dimensional representation we make use of the recently developed method to extract nonlinear RCs from the reweighted path ensemble (RPE) [8,9].…”