Breakthrough Molecular Dynamics Research via an Anton2 Supercomputer

项目摘要 2010年，匹兹堡超级计算中心(PSC)和D.E.Shaw Research(DESRES)合作制作了 安东专用分子动力学(MD)超级计算机可用于国家生物医学研究 社区，这是第一次。Anton使研究人员能够模拟生物分子系统两个数量级 速度比任何传统超级计算机都快，使研究人员能够访问关键的多个 微秒和更长的时间尺度，大多数具有生物学意义的分子过程都发生在这些时间尺度上。在……里面 2016年，在NIH的运营支持下，DESRES在PSC提供了下一代Anton 2系统，地址为 免费的。这笔来自DESRES的数百万美元的礼物，在NIH的支持下，为 研究人员将通过模拟大到 以每天数微秒的速度发射70万个原子。这个重建项目的目标是提供 国家生物医学研究社区，继续访问这一独特而强大的Anton 2资源 并最大限度地利用这一资源造福社会。自2010年以来，PSC已经资助了589项研究 由PSC托管的Anton系统上的202个独特的私人投资促进机构开展的项目。到目前为止，这些项目已经 产生了292份出版物，其中许多对他们的研究领域产生了重大影响。这些字段 涵盖构成生物学基本基础的生物分子过程的整个光谱， 包括蛋白质折叠、离子通道选择性和门控、膜动力学和组织、蛋白质- 配体结合，以及许多其他的。对Anton 2的需求相当高，需求是可以满足的2-3倍 每年。有鉴于此，我们的目标不仅集中在提供持续的访问上，而且还集中在最大化 这一有限资源对社区的价值-认识到广泛、多样化的安东的创造力 2研究社区是我们最强大的创新资源之一。Anton 2将作为一个 XSEDE服务提供商，Anton 2的可及性和影响力将通过参与 他们广泛的扩大参与、外展和培训计划。通过这些外展努力， 更多机构的研究人员将有机会使用Anton 2，特别是来自 在生物医学研究中，传统上代表不足的群体。数百个长时间尺度的MD轨迹 研究人员在Anton 2上生成的唯一且有价值的数据集可用于获得更多 生物医学知识，推进机器学习协议在分子增强中的应用 动力学模拟。这一重要的数据集将通过以下方式向世界各地的研究人员和教育工作者提供 一个门户网站，同设在PSC的Bridges-2系统上，用于课堂教学和研究，包括 再分析、机器学习和数据挖掘。

Project Summary In 2010, Pittsburgh Supercomputing Center (PSC) and D.E. Shaw Research (DESRES) partnered to make the Anton special-purpose molecular dynamics (MD) supercomputer available to the national biomedical research community for the first time. Anton enabled researchers to simulate biomolecular systems two orders of magnitude faster than any conventional supercomputer, allowing researchers access to critical multi- microsecond and longer timescales on which most biologically-significant molecular processes take place. In 2016, with operational support from NIH, DESRES made available a next generation Anton 2 system at PSC at no cost. This multimillion-dollar gift from DESRES, with NIH support, provided a unique opportunity for researchers to tackle even more groundbreaking biological questions by simulating systems as large as 700,000 atoms at a rate of multiple microseconds per day. The goal of this renewal project is to provide the national biomedical research community with continued access to this unique and powerful Anton 2 resource and to maximize the benefit of this resource to the community. Since 2010, PSC has supported 589 research projects conducted by 202 unique PIs on the Anton systems hosted at PSC. So far, these projects have resulted in 292 publications, many of which have had significant impact on their fields of research. These fields cover the entire spectrum of biomolecular processes that form the fundamental underpinnings of biology, including protein folding, ion channel selectivity and gating, membrane dynamics and organization, protein- ligand binding, and many others. Demand for Anton 2 is quite high, with 2-3x higher demand than can be met each year. Given this, our goals are focused not only on providing continued access but also on maximizing the value of this limited resource to the community—recognizing that the creativity of the broad, diverse Anton 2 research community is one of our most powerful resources for innovation. Anton 2 will be integrated as an XSEDE service provider, and the accessibility and impact of Anton 2 will significantly increase by engaging in their extensive broadening participation, outreach, and training programs. Through these outreach efforts, researchers at many more institutions will have the opportunity to use Anton 2, especially researchers from traditionally underrepresented groups in biomedical research. The hundreds of long-timescale MD trajectories researchers generate on Anton 2 constitute a unique and valuable dataset that can be used to gain additional biomedical knowledge and advance the application of machine learning protocols to augment molecular dynamics simulations. This important dataset will be available to researchers and educators worldwide through a web portal and co-located on the PSC's Bridges-2 system for classroom instruction and research, including reanalysis, machine learning, and data mining.