Vivekanandan Balasubramanian

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Replica exchange molecular dynamics has emerged as a powerful tool for efficiently sampling free energy landscapes for conformational and chemical transitions. However, daunting challenges remain in efficiently getting such simulations to scale to the very large number of replicas required to address problems in state spaces beyond two dimensions. The(More)
There are many science applications that require scalable task-level parallelism, support for flexible execution and coupling of ensembles of simulations. Most high-performance system software and middleware, however, are designed to support the execution and optimization of single tasks. Motivated by the missing capabilities of these computing systems and(More)
For many macromolecular systems the accurate sampling of the relevant regions on the potential energy surface cannot be obtained by a single, long Molecular Dynamics (MD) trajectory. New approaches are required to promote more efficient sampling. We present the design and implementation of the Extensible Toolkit for Advanced Sampling and analYsis (ExTASY)(More)
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