Comparison of sampling efficiency between simulated tempering and replica exchange
نویسندگان
چکیده
منابع مشابه
Enhanced Monte Carlo Sampling through Replica Exchange with Solute Tempering
With a view to improving the consistency of free energy perturbation calculations in Monte Carlo simulations of protein-ligand complexes, we have implemented the replica exchange with solute tempering (REST) method in the MCPRO software. By augmenting the standard REST approach with regular attempted jumps in selected dihedral angles, our combined method facilitates sampling of ligand binding m...
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We apply the recently developed replica exchange with solute tempering (REST) to three large solvated peptide systems: an alpha-helix, a beta-hairpin, and a TrpCage, with these peptides defined as the "central group". We find that our original implementation of REST is not always more efficient than the replica exchange method (REM). Specifically, we find that exchanges between folded (F) and u...
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Simulated tempering distributed replica sampling (STDR) is a generalized-ensemble method designed specifically for simulations of large molecular systems on shared and heterogeneous computing platforms [Rauscher, Neale and Pomès (2009) J. Chem. Theor. Comput. 5, 2640]. The STDR algorithm consists of an alternation of two steps: (1) a short molecular dynamics (MD) simulation; and (2) a stochasti...
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Multimodal structures in the sampling density (e.g. two competing phases) can be a serious problem for traditional Markov Chain Monte Carlo (MCMC), because correct sampling of the different structures can only be guaranteed for infinite sampling time. Samples may not decouple from the initial configuration for a long time and autocorrelation times may be hard to determine. We analyze a suitable...
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We discuss multidimensional generalizations of multicanonical algorithm, simulated tempering, and replica-exchange method. We generalize the original potential-energy function E0 by adding any physical quantity V of interest as a new energy term with a coupling constant lambda. We then perform a multidimensional multicanonical simulation where a random walk in E0 and V spaces is realized. We ca...
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ژورنال
عنوان ژورنال: The Journal of Chemical Physics
سال: 2008
ISSN: 0021-9606,1089-7690
DOI: 10.1063/1.2988339