Replica Exchange of Self-Guided Langevin Dynamics Simulation
نویسندگان
چکیده
منابع مشابه
Protein Folding Simulations Combining Self-Guided Langevin Dynamics and Temperature-Based Replica Exchange.
Computer simulations are increasingly being used to predict thermodynamic observables for folding small proteins. Key to continued progress in this area is the development of algorithms that accelerate conformational sampling. Temperature-based replica exchange (ReX) is a commonly used protocol whereby simulations at several temperatures are simultaneously performed and temperatures are exchang...
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Replica exchange molecular dynamics (REMD) method is one of the generalized-ensemble algorithms which performs random walk in energy space and helps a system to escape from local energy traps. In this work, we studied the accuracy and efficiency of REMD by examining its ability to reproduce the results of multiple extended conventional molecular dynamics (MD) simulations and to enhance conforma...
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Introduction Oligo(m-phenyleneethynylene)s, shown in Figure 1, have been shown to undergo a solvent-driven transition from a random conformation in low polarity solvents to an α-helix conformation in polar solvents as a result of solvophobic interactions. 2 However, a detailed atomic-level study of the effects of specific intermolecular interactions, such as hydrogen bonding, van der Waals and ...
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ژورنال
عنوان ژورنال: Biophysical Journal
سال: 2012
ISSN: 0006-3495
DOI: 10.1016/j.bpj.2011.11.930