High-Throughput All-Atom Molecular Dynamics Simulations Using Distributed Computing
High-Throughput All-Atom Molecular Dynamics Simulations Using Distributed Computing
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DOI：
10.1021/ci900455r
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发表时间：
2010-03-01
影响因子：
5.6
通讯作者：
De Fabritiis, G.
中科院分区：
文献类型：
--
作者：
Buch, I.;Harvey, M. J.;De Fabritiis, G.
尽管分子动力学模拟方法在大分子系统建模中很有用，但它们的计算成本仍然很高，生产工作需要昂贵的高性能计算（HPC）资源。我们回顾了在图形处理单元（GPU）上加速分子动力学的最新创新，并描述了GPUGRID，一个使用非专用桌面和工作站计算机的GPU资源的志愿者计算项目。特别是，我们展示了模拟数以千计的全原子分子轨迹的能力，每个轨迹平均产生20纳秒/天（对于类似于30,000 - 80,000个原子的系统）。结合用于计算结合自由能的平均力势（PMF）协议，我们展示了GPUGRID在计算Src SH2结构域/pYEEI配体复合物的精确结合亲和力方面的使用，通过重建373个伞式采样窗口（每个55 ns）的PMF（总数据的20.5 μ s）。在0.7 kcal/mol范围内得到了-8.7 +/- 0.4 kcal/mol的标准结合自由能。该基础设施将为高通量准确的结合亲和力预测提供强大的系统基础。
Although molecular dynamics simulation methods are useful in the modeling of macromolecular systems, they remain computationally expensive, with production work requiring costly high-performance computing (HPC) resources. We review recent innovations in accelerating molecular dynamics on graphics processing units (GPUs), and we describe GPUGRID, a volunteer computing project that uses the GPU resources of nondedicated desktop and workstation computers. In particular, we demonstrate the capability of simulating thousands of all-atom molecular trajectories generated at an average of 20 ns/day each (for systems of similar to 30 000-80 000 atoms). In conjunction with a potential of mean force (PMF) protocol for computing binding free energies, we demonstrate the use of GPUGRID in the computation of accurate binding affinities of the Src SH2 domain/pYEEI ligand complex by reconstructing the PMF over 373 umbrella sampling windows of 55 ns each (20.5 mu s of total data). We obtain a standard free energy of binding of -8.7 +/- 0.4 kcal/mol within 0.7 kcal/mol from experimental results. This infrastructure will provide the basis for a robust system for high-throughput accurate binding affinity prediction.