We discuss the possibility of implementing asynchronous replica-exchange (or parallel tempering) molecular dynamics. In our scheme, the exchange attempts are driven by asynchronous messages sent by one of the computing nodes, so that different replicas are allowed to perform a different number, of time, steps between subsequent attempts. The implementation is simple and based on the message-passing interface (MPI). illustrate the advantages of our scheme with respect to the standard synchronous algorithm and we benchmark it for a model Lennard-Jones liquid on an IBM-LS21 blade center cluster
We study generalizations of parallel tempering, also known as replica exchange method, that aim at m...
We sketch the statistical physics framework of the replica exchange technique when applied to molecu...
We present microcanonical replica exchange molecular dynamics simulations as an alternative to canon...
Abstract — Replica exchange is a powerful sampling algorithm and can be effectively used for applica...
Parallel tempering (or the replica exchange method (REM)) is a powerful method for speeding up the s...
Abstract — This paper presents Salsa, a novel, decentralized and asynchronous realization of the “re...
We address the question of constructing a protocol for replica-exchange molecular dynamics (REMD) si...
We study the dynamics of parallel tempering simulations, also known as the replica exchange techniqu...
We present an approach to mimic replica exchange molecular dynamics simulations (REMD) on a microsec...
We developed a replica exchange method that is effectively parallelizable even if the computational ...
Replica Exchange (RE) simulations have emerged as an important algorithmic tool for the molecular s...
A replica exchange Markov Chain Monte Carlo engine is proposed and implemented with automatic temper...
21 pages, 14 figures, 5 tablesInternational audienceMetastability is a common obstacle to performing...
The purpose of this article is to lay the mathematical foundations of a well known numerical approac...
AbstractToday's standard molecular dynamics simulations of moderately sized biomolecular systems at ...
We study generalizations of parallel tempering, also known as replica exchange method, that aim at m...
We sketch the statistical physics framework of the replica exchange technique when applied to molecu...
We present microcanonical replica exchange molecular dynamics simulations as an alternative to canon...
Abstract — Replica exchange is a powerful sampling algorithm and can be effectively used for applica...
Parallel tempering (or the replica exchange method (REM)) is a powerful method for speeding up the s...
Abstract — This paper presents Salsa, a novel, decentralized and asynchronous realization of the “re...
We address the question of constructing a protocol for replica-exchange molecular dynamics (REMD) si...
We study the dynamics of parallel tempering simulations, also known as the replica exchange techniqu...
We present an approach to mimic replica exchange molecular dynamics simulations (REMD) on a microsec...
We developed a replica exchange method that is effectively parallelizable even if the computational ...
Replica Exchange (RE) simulations have emerged as an important algorithmic tool for the molecular s...
A replica exchange Markov Chain Monte Carlo engine is proposed and implemented with automatic temper...
21 pages, 14 figures, 5 tablesInternational audienceMetastability is a common obstacle to performing...
The purpose of this article is to lay the mathematical foundations of a well known numerical approac...
AbstractToday's standard molecular dynamics simulations of moderately sized biomolecular systems at ...
We study generalizations of parallel tempering, also known as replica exchange method, that aim at m...
We sketch the statistical physics framework of the replica exchange technique when applied to molecu...
We present microcanonical replica exchange molecular dynamics simulations as an alternative to canon...