Cellular and Molecular Biology.
Biochemistry and Molecular Biology.
Brief Bioinform. 2018 Sep 28;19(5):853-862. doi: 10.1093/bib/bbx006.
Molecular dynamics (MD) simulation allows one to predict the time evolution of a system of interacting particles. It is widely used in physics, chemistry and biology to address specific questions about the structural properties and dynamical mechanisms of model systems. MD earned a great success in genome research, as it proved to be beneficial in sorting pathogenic from neutral genomic mutations. Considering their computational requirements, simulations are commonly performed on HPC computing devices, which are generally expensive and hard to administer. However, variables like the software tool used for modeling and simulation or the size of the molecule under investigation might make one hardware type or configuration more advantageous than another or even make the commodity hardware definitely suitable for MD studies. This work aims to shed lights on this aspect.
分子动力学（MD）模拟允许人们预测相互作用粒子系统的时间演化。它在物理学、化学和生物学中被广泛用于解决关于模型系统结构性质和动力学机制的具体问题。MD 在基因组研究中取得了巨大的成功，因为它被证明有助于从中性基因组突变中筛选出致病突变。考虑到它们的计算需求，模拟通常在高性能计算（HPC）计算设备上进行，这些设备通常昂贵且难以管理。然而，用于建模和模拟的软件工具或研究的分子大小等变量可能会使一种硬件类型或配置比另一种更有利，甚至使普通硬件非常适合 MD 研究。这项工作旨在阐明这一方面。
