Aksimentiev组

NAMD是一个分子动力学程序设计高性能的模拟非常大的生物对象基于CPU和GPU的体系结构。NAMD千兆级并行超级计算机上提供了可扩展的性能组成的成千上万的核心,以及廉价的商品集群在学术环境中普遍存在。它是用c++写的,靠魅力+ +并行对象为获得最佳性能在低延迟架构。NAMD是一个多功能,多用途的代码集先进的算法进行模拟在恰当的热力学乐团,使用广受欢迎的CHARMM,琥珀,OPLS, GROMOS biomolec——佩珀力场。在这里,我们审查的主要特色NAMD允许平衡和enhanced-sampling分子动力学模拟与计算效率。我们描述底层NAMD利用的概念及其实现,尤其是处理远程静电学;控制温度、压力、和pH值;定制的网格应用外部势;利用多重副本模拟大规模并行资源;和混合量子力学/ molecular-mechanical描述。 We detail the variety of options offered by NAMD for enhanced-sampling simulations aimed at determining free-energy differences of either alchem- ical or geometrical transformations and outline their applicability to specific problems. Last, we discuss the roadmap for the development of NAMD and our current efforts toward achieving optimal performance on GPU-based architectures, for pushing back the limitations that have prevented biologically realistic billion-atom objects to be fruitfully simulated, and for making large-scale simulations less expensive and easier to set up, run, and analyze. NAMD is distributed free of charge with its source code at www.ks.uiuc.edu.