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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). We 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.
The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated in a Hamil
New hardware architectures open up immense opportunities for supercomputer simulations. However, programming techniques for different architectures vary significantly, which leads to the necessity of developing and supporting multiple co
Redox processes are important in chemistry, with applications in biomedicine, chemical analysis, among others. As many redox experiments are also performed at a fixed value of pH, having an efficient computational method to support experimental measu
This paper presents an asynchronous incremental aggregated gradient algorithm and its implementation in a parameter server framework for solving regularized optimization problems. The algorithm can handle both general convex (possibly non-smooth) reg
The parallel annealing method is one of the promising approaches for large scale simulations as potentially scalable on any parallel architecture. We present an implementation of the algorithm on the hybrid program architecture combining CUDA and MPI