منابع مشابه
Serial replica exchange.
Parallel tempering (or the replica exchange method (REM)) is a powerful method for speeding up the sampling of conformational states of systems with rough energy landscapes, like proteins, where stable conformational states can be separated by large energy barriers. The usual implementation of the REM is performed on local computer clusters (or parallel processors) where the different replicas ...
متن کاملGeneralized replica exchange method.
We present a powerful replica exchange method, particularly suited to first-order phase transitions associated with the backbending in the statistical temperature, by merging an optimally designed generalized ensemble sampling with replica exchanges. The key ingredients of our method are parametrized effective sampling weights, smoothly joining ordered and disordered phases with a succession of...
متن کاملReplica-Exchange Cluster Algorithm
In finite-size scaling analyses of Monte Carlo simulations of second-order phase transitions one often needs an extended temperature/energy range around the critical point. By combining the replica-exchange algorithm with cluster updates and an adaptive routine to find the range of interest, we introduce a new flexible and powerful method for systematic investigations of critical phenomena. As ...
متن کاملImplementation of a Serial Replica Exchange Method in a Physics-Based United-Residue (UNRES) Force Field.
The kinetic-trapping problem in simulating protein folding can be overcome by using a Replica Exchange Method (REM). However, in implementing REM in molecular dynamics simulations, synchronization between processors on parallel computers is required, and communication between processors limits its ability to sample conformational space in a complex system efficiently. To minimize communication ...
متن کاملReplica exchange with dynamical scaling.
A replica exchange method is presented which requires fewer replicas and is designed to be used for large systems. In this method, dynamically scaled replicas are placed between conventional replicas at broadly spaced temperatures. The potential of the scaled replicas is linearly scaled by a dynamical variable which varies between 0 and 1. When the variable is near either end point the replica ...
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ژورنال
عنوان ژورنال: The Journal of Physical Chemistry B
سال: 2007
ISSN: 1520-6106,1520-5207
DOI: 10.1021/jp064479e