GALAMOST: GPU‐accelerated large‐scale molecular simulation toolkit
GALAMOST: GPU‐accelerated large‐scale molecular simulation toolkit
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DOI：
10.1002/jcc.23365
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发表时间：
2013-09
影响因子：
3
通讯作者：
Youliang Zhu;Hong Liu;Zhan-Wei Li;H. Qian;G. Milano;Zhong-yuan Lu
中科院分区：
文献类型：
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作者：
Youliang Zhu;Hong Liu;Zhan-Wei Li;H. Qian;G. Milano;Zhong-yuan Lu
GALAMOST（图形处理单元（GPU）加速的大规模分子模拟工具包）是一个分子模拟软件包，旨在利用GPU的计算能力。除了分子动力学（MD）软件包的共同特点外，它还专门用于研究聚合物体系在介观尺度下的自组装，相变和其他性质，并使用一些最新开发的模拟技术。为了加速模拟，GALAMOST包含一种混合粒子场MD技术，其中粒子与粒子之间的相互作用被粒子与密度场的相互作用取代。此外，通过自底向上粗粒化方法获得的数值势可以在GALAMOST模拟中实现。通过将这些力场和GALAMOST中的粒子-密度耦合方法相结合，可以在很长的模拟时间内以非常大的系统尺寸进行聚合物的模拟。此外，GALAMOST包含两个具体模型，即软各向异性颗粒模型和链生长聚合模型，通过它们可以分别研究软各向异性颗粒的分级自组装和与聚合相关的问题。文中详细介绍了GALAMOST的GPU优化算法、封装特性和性能测试。© 2013 Wiley Periodicals，Inc.
GALAMOST [graphics processing unit (GPU)‐accelerated large‐scale molecular simulation toolkit] is a molecular simulation package designed to utilize the computational power of GPUs. Besides the common features of molecular dynamics (MD) packages, it is developed specially for the studies of self‐assembly, phase transition, and other properties of polymeric systems at mesoscopic scale by using some lately developed simulation techniques. To accelerate the simulations, GALAMOST contains a hybrid particle‐field MD technique where particle–particle interactions are replaced by interactions of particles with density fields. Moreover, the numerical potential obtained by bottom‐up coarse‐graining methods can be implemented in simulations with GALAMOST. By combining these force fields and particle‐density coupling method in GALAMOST, the simulations for polymers can be performed with very large system sizes over long simulation time. In addition, GALAMOST encompasses two specific models, that is, a soft anisotropic particle model and a chain‐growth polymerization model, by which the hierarchical self‐assembly of soft anisotropic particles and the problems related to polymerization can be studied, respectively. The optimized algorithms implemented on the GPU, package characteristics, and benchmarks of GALAMOST are reported in detail. © 2013 Wiley Periodicals, Inc.