Roadmaps through Free Energy Landscapes Calculated Using the Multidimensional vFEP Approach
نویسندگان
چکیده
منابع مشابه
Capturing Molecular Energy Landscapes with Probabilistic Conformational Roadmaps
Probabilistic roadmaps are an effective tool to compute the connectivity of the collision-free subset of high-dimensional robot configuration space. This paper extends them to capture the pertinent features of continuous functions over high-dimensional spaces. This extension has several possible applications, but the focus here is on computing energetically favorable motions of bio-molecules. M...
متن کاملEnhanced Sampling of Multidimensional Free-Energy Landscapes Using Adaptive Biasing Forces
We propose an adaptive biasing algorithm aimed at enhancing the sampling of multimodal measures by Langevin dynamics. The underlying idea consists in generalizing the standard adaptive biasing force method commonly used in conjunction with molecular dynamics to handle in a more effective fashion multidimensional reaction coordinates. The proposed approach is anticipated to be particularly usefu...
متن کاملTopographical complexity of multidimensional energy landscapes.
A scheme for visualizing and quantifying the complexity of multidimensional energy landscapes and multiple pathways is presented employing principal component-based disconnectivity graphs and the Shannon entropy of relative "sizes" of superbasins. The principal component-based disconnectivity graphs incorporate a metric relationship between the stationary points of the system, which enable us t...
متن کاملEnergy Landscapes of Multidimensional Random Fourier Series
To any positive number ε and any nonnegative even Schwartz function w : R → R we associate the random function u on them-torus T := R/Z defined as the real part of the random Fourier series ∑ ~ν∈Zm X~ν,ε exp(2πi~ν · ~ θ), whereX~ν,ε are complex independent Gaussian random variables with variancew(ε|~ν|). LetN denote the number of critical points of u. We describe explicitly two constantsC,C′ su...
متن کاملCalculation of free energy landscapes: A histogram reweighted metadynamics approach
We present an efficient method for the calculation of free energy landscapes. Our approach involves a history-dependent bias potential, which is evaluated on a grid. The corresponding free energy landscape is constructed via a histogram reweighting procedure a posteriori. Because of the presence of the bias potential, it can be also used to accelerate rare events. In addition, the calculated fr...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Journal of Chemical Theory and Computation
سال: 2013
ISSN: 1549-9618,1549-9626
DOI: 10.1021/ct400691f