Collaborative Research SI2-SSE: Sustained Innovation in Acceleration of Molecular Dynamics on Future Computational Environments: Power to the People in the Cloud and on Accelerator

这个由加州圣地亚哥大学圣地亚哥超级计算机中心、佛罗里达大学量子理论项目和工业合作伙伴NVIDIA、英特尔和亚马逊共同合作的项目，专注于开发创新、用于加速凝聚相分子动力学（MD）的全面开源软件元素库使用下一代加速器硬件（包括英特尔的MIC系统和图形处理单元（GPU））模拟生物分子。它将扩展支持，包括所有主要的MD技术，并开发开源加速分析库。一个优先事项是加强采样技术，包括热力学积分，恒定pH值算法，多维哈密顿量交换和Metadaptics。然后，这些元素将与亚马逊合作，通过易于访问的Web前端到云服务（包括亚马逊的EC2 GPU硬件）来支持MD即服务。将大规模MD工作流程从需要访问大型超级计算机硬件转变为所有桌面和云资源都可以访问，提供了关键的软件基础设施，以支持化学，生命科学，材料科学，环境和可再生能源领域的变革性研究。通过该项目创建的软件元素具有极其广泛的影响。AMBER软件集成了对下一代硬件加速的全面支持，这使大量用户受益。从独特的IP和800个使用AMBER MD引擎的网站下载了超过10，000个最新的AMBER Tools包，证明了这项工作影响的研究人员社区的范围。开发简单的基于Web的前端，以使用弹性可扩展的云资源，使模拟成为所有研究人员的常规。与此同时，教育和推广工作不仅培训了下一代科学家如何使用这里开发的MD加速库和先进的MD模拟技术，而且还让他们思考如何改变他们的方法，因为以前仅限于大型超级计算机的性能现在可以在个人桌面上使用。

This collaborative project between the San Diego Supercomputer Center at the University of California San Diego, the Quantum Theory Project at the University of Florida and industrial partners NVIDIA, Intel and Amazon is focused on developing innovative, comprehensive open source software element libraries for accelerating condensed phase Molecular Dynamics (MD) simulations of biomolecules using next generation accelerator hardware including Intel's MIC system and Graphics Processing Units (GPU). It will extend support to include all major MD techniques and develop open source accelerated analysis libraries. A priority is enhanced sampling techniques including Thermodynamic Integration, constant pH algorithms, Multi-Dimensional Hamiltonian Replica Exchange and Metadynamics. These elements will then be combined, in collaboration with Amazon to support MD as-a-service through easily accessible web front ends to cloud services, including Amazon's EC2 GPU hardware. Transitioning large scale MD workflows from requiring access to large supercomputer hardware to being accessible to all on desktop and cloud resources provides the critical software infrastructure to support transformative research in the fields of chemistry, life science, materials science, environmental and renewable energy.The software elements created through this project have an extremely broad impact. The integration of comprehensive support for next generation hardware acceleration into the AMBER software alone benefits a very large user base. With over 10,000 downloads of the latest AMBER Tools package from unique IPs and 800 sites using the AMBER MD engines testify to the scope of the community of researchers this work impacts. The development of simple web based front ends for use of elastically scalable cloud resources makes simulations routine for all researchers. Meanwhile education and outreach efforts train the next generation of scientists not just in how to use the MD acceleration libraries and advanced MD simulation techniques developed here but also gets them thinking about how their approach can be transformed given that performance that was previously restricted to large scale supercomputers is now available on individual desktops.