Replica exchange molecular dynamics has emerged as a powerful tool for efficiently sampling free ... more 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 development of enabling technology to carry out such simulations is in its infancy, and thus it remains an open question as to which applications demand extension into higher dimensions. In the present work, we explore this problem space by applying asynchronous Hamiltonian replica exchange molecular dynamics with a combined quantum mechanical/molecular mechanical potential to explore the conformational space for a simple ribonucleoside. This is done using a newly developed software framework capable of executing >3,000 replicas with only enough resources to run 2,000 simultaneously. This may not be possible with traditional synchronous replica exchange approaches. Our results demonstrate 1.) the necessity of high dimensional sampling simulations for biological systems, even as simple as a single ribonucleoside, and 2.) the utility of asynchronous exchange protocols in managing simultaneous resource requirements expected in high dimensional sampling simulations. It is expected that more complicated systems will only increase in computational demand and complexity, and thus the reported asynchronous approach may be increasingly beneficial in order to make such applications available to a broad range of computational scientists.
The Extended Collaborative Support Service (ECSS) of XSEDE is a program to provide support for ad... more The Extended Collaborative Support Service (ECSS) of XSEDE is a program to provide support for advanced user requirements that cannot and should not be supported via a regular ticketing system. Recently, two ECSS projects have been awarded by XSEDE management to support the high-throughput of high-performance (HTHP) molecular dynamics (MD) simulations; both of these ECSS projects use a SAGA-based Pilot-Jobs approach as the technology required to support the HTHP scenarios. Representative of the underlying ECSS philosophy, these projects were envisioned as three-way collaborations between the application stakeholders, advanced/research software development team, and the resource providers. In this paper, we describe the aims and objectives of these ECSS projects, how the deliverables have been met, and some preliminary results obtained. We believe the structure of the ECSS program enables targeted projects that address missing gaps in making distributed cyberinfrastructure systems more productive. We also describe how SAGA has been deployed on XSEDE in Community Software Area as a necessary precursor for these projects.
Replica exchange molecular dynamics has emerged as a powerful tool for efficiently sampling free ... more 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 development of enabling technology to carry out such simulations is in its infancy, and thus it remains an open question as to which applications demand extension into higher dimensions. In the present work, we explore this problem space by applying asynchronous Hamiltonian replica exchange molecular dynamics with a combined quantum mechanical/molecular mechanical potential to explore the conformational space for a simple ribonucleoside. This is done using a newly developed software framework capable of executing >3,000 replicas with only enough resources to run 2,000 simultaneously. This may not be possible with traditional synchronous replica exchange approaches. Our results demonstrate 1.) the necessity of high dimensional sampling simulations for biological systems, even as simple as a single ribonucleoside, and 2.) the utility of asynchronous exchange protocols in managing simultaneous resource requirements expected in high dimensional sampling simulations. It is expected that more complicated systems will only increase in computational demand and complexity, and thus the reported asynchronous approach may be increasingly beneficial in order to make such applications available to a broad range of computational scientists.
The Extended Collaborative Support Service (ECSS) of XSEDE is a program to provide support for ad... more The Extended Collaborative Support Service (ECSS) of XSEDE is a program to provide support for advanced user requirements that cannot and should not be supported via a regular ticketing system. Recently, two ECSS projects have been awarded by XSEDE management to support the high-throughput of high-performance (HTHP) molecular dynamics (MD) simulations; both of these ECSS projects use a SAGA-based Pilot-Jobs approach as the technology required to support the HTHP scenarios. Representative of the underlying ECSS philosophy, these projects were envisioned as three-way collaborations between the application stakeholders, advanced/research software development team, and the resource providers. In this paper, we describe the aims and objectives of these ECSS projects, how the deliverables have been met, and some preliminary results obtained. We believe the structure of the ECSS program enables targeted projects that address missing gaps in making distributed cyberinfrastructure systems more productive. We also describe how SAGA has been deployed on XSEDE in Community Software Area as a necessary precursor for these projects.
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Papers by Melissa Romanus