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Title: Constraint methods that accelerate free-energy simulations of biomolecules

Atomistic molecular dynamics simulations of biomolecules are critical for generating narratives about biological mechanisms. The power of atomistic simulations is that these are physics-based methods that satisfy Boltzmann’s law, so they can be used to compute populations, dynamics, and mechanisms. But physical simulations are computationally intensive and do not scale well to the sizes of many important biomolecules. One way to speed up physical simulations is by coarse-graining the potential function. Another way is to harness structural knowledge, often by imposing spring-like restraints. But harnessing external knowledge in physical simulations is problematic because knowledge, data, or hunches have errors, noise, and combinatoric uncertainties. Here, we review recent principled methods for imposing restraints to speed up physics-based molecular simulations that promise to scale to larger biomolecules and motions.
Authors:
 [1] ;  [2] ;  [1] ;  [3] ;  [1] ;  [3]
  1. Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794 (United States)
  2. Department of Chemistry, University of Calgary, Calgary, Alberta T2N 1N4 (Canada)
  3. (United States)
Publication Date:
OSTI Identifier:
22493382
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Chemical Physics; Journal Volume: 143; Journal Issue: 24; Other Information: (c) 2015 AIP Publishing LLC; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
United States
Language:
English
Subject:
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS; 37 INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY; BOLTZMANN EQUATION; COMPUTERIZED SIMULATION; ERRORS; FREE ENERGY; LIMITING VALUES; MOLECULAR DYNAMICS METHOD; NOISE; POTENTIALS; RESTRAINTS; REVIEWS; VELOCITY