Replica-exchange simulated tempering method for simulations of frustrated systems
نویسندگان
چکیده
منابع مشابه
From multidimensional replica-exchange method to multidimensional multicanonical algorithm and simulated tempering.
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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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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An innovative replica exchange (parallel tempering) method called replica exchange with solute tempering (REST) for the efficient sampling of aqueous protein solutions is presented here. The method bypasses the poor scaling with system size of standard replica exchange and thus reduces the number of replicas (parallel processes) that must be used. This reduction is accomplished by deforming the...
متن کاملReplica exchange with solute scaling: a more efficient version of replica exchange with solute tempering (REST2).
A small change in the Hamiltonian scaling in Replica Exchange with Solute Tempering (REST) is found to improve its sampling efficiency greatly, especially for the sampling of aqueous protein solutions in which there are large-scale solute conformation changes. Like the original REST (REST1), the new version (which we call REST2) also bypasses the poor scaling with system size of the standard Te...
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An asynchronous implementation of the replica exchange method that addresses some of the limitations of conventional synchronous replica exchange implementations is presented. In asynchronous replica exchange pairs of processors initiate and perform temperature replica exchanges independently from the other processors, thereby removing the need for processor synchronization found in conventiona...
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ژورنال
عنوان ژورنال: Chemical Physics Letters
سال: 2000
ISSN: 0009-2614
DOI: 10.1016/s0009-2614(00)01262-8