Replica exchange with nonequilibrium switches
نویسندگان
چکیده
منابع مشابه
Replica 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...
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 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...
متن کاملSerial 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 کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Proceedings of the National Academy of Sciences
سال: 2009
ISSN: 0027-8424,1091-6490
DOI: 10.1073/pnas.0900406106