3E1110 Replica-exchange interface program (REIN)(Proteins:Structure,Oral Presentation)
نویسندگان
چکیده
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 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 ...
متن کاملReplica exchange with nonequilibrium switches.
We introduce a replica exchange (parallel tempering) method in which attempted configuration swaps are generated using nonequilibrium work simulations. By effectively increasing phase space overlap, this approach mitigates the need for many replicas. We illustrate our method by using a model system and show that it is able to achieve the computational efficiency of ordinary replica exchange, us...
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ژورنال
عنوان ژورنال: Seibutsu Butsuri
سال: 2012
ISSN: 0582-4052,1347-4219
DOI: 10.2142/biophys.52.s65_4