title: Leveraging the Information from Markov State Models To Improve the Convergence of Umbrella Sampling Simulations.
abstract: Umbrella sampling (US) simulation is a highly effective method for sampling the conformations of a complex system within a small subspace of predefined coordinates. In a typical US stratification strategy, biasing "window" potentials spanning the subspace of interest are introduced to narrow down the range of accessible conformations and accelerate the sampling. The speed of convergence in each biased window simulation may, however, differ. For example, windows that coincide with a large energetic barrier along a coordinate that is orthogonal to the predefined subspace are often plagued by slow relaxation timescales. Here, we design a method that can quantitatively detect this type of issue and gain further insight into the origin of the slow relaxation timescale. Once the problematic windows affected by slow convergence are identified, additional simulations limited to only these windows can be carried out, thereby reducing the overall computational effort. Several possible approaches aimed at performing US simulations adaptively are discussed, and their respective performance is illustrated using a simple model system. Last, simulations of an atomic deca-alanine system are used to demonstrate the efficacy of analyzing US simulation trajectories using the proposed method.
authors.affiliation: Leadership Computing Facility, Argonne National Laboratory , 9700 Cass Avenue, Building 240, Argonne, Illinois 60439, United States.
authors.forename: Sunhwan
authors.initials: S
authors.lastname: Jo
authors.affiliation: Department of Chemistry, University of Chicago , Chicago, Illinois 60637, United States.
authors.forename: Donghyuk
authors.initials: D
authors.lastname: Suh
authors.affiliation: Department of Chemistry, University of Chicago , Chicago, Illinois 60637, United States.
authors.forename: Ziwei
authors.initials: Z
authors.lastname: He
authors.affiliation: Laboratoire International Associé Centre National de la Recherche Scientifique and University of Illinois at Urbana-Champaign, UMR 7565, Université de Lorraine , BP 70239, 54506 Vandœuvre-lès-Nancy, France.|Department of Physics and Beckman Institute for Advanced Research and Technology, University of Illinois at Urbana-Champaign , 1110 West Green Street, 405 North Mathews, Urbana, Illinois 61801, United States.
authors.forename: Christophe
authors.initials: C
authors.lastname: Chipot
authors.affiliation: Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago , Chicago, Illinois 60637, United States.|Center for Nanomaterials, Argonne National Laboratory , Argonne, Illinois 60439, United States.
authors.forename: Benoît
authors.initials: B
authors.lastname: Roux