libxtc: an efficient library for reading XTC-compressed MD trajectory data.
libxtc: an efficient library for reading XTC-compressed MD trajectory data.
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DOI：
10.1186/s13104-021-05536-5
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发表时间：
2021-04-01
影响因子：
1.8
通讯作者：
Efremov RG
中科院分区：
文献类型：
--
作者：
Krylov NA;Efremov RG
这项工作的目的是优化处理的分子动力学（MD）的轨迹数据获得的大型生物分子系统。两个流行的软件工具被选为参考：tng和xdrfile库。当前tng算法和库的实现要么快要么存储效率高，xdrfile存储效率高但速度慢。我们的目标是通过修改xdr文件的代码来将联合收割机速度和存储效率结合起来。在这里，我们提出了libxtc，一个现成的使用库阅读MD轨迹文件的xtc格式。libxtc的有效性证明了几个不同大小的生物分子系统（~ 2 × 104 ~ 2 × 105原子）。在顺序模式下，libxtc的性能分别比xdrfile和tng高1.8倍和低1.4倍。在并行模式下，libxtc比xdrfile和tng快3倍和1.3倍。与此同时，以xtc格式存储的MD数据需要的磁盘空间比以最快阅读模式使用tng算法处理的数据少1.3倍，这是一个显著的节省，特别是当MD轨迹较长且原子数量较大时-这适用于大多数生物相关系统。在线版本包含补充材料，可通过10.1186/s13104-021-05536-5获得。
The purpose of this work is to optimize the processing of molecular dynamics (MD) trajectory data obtained for large biomolecular systems. Two popular software tools were chosen as the reference: the tng and the xdrfile libraries. Current implementation of tng algorithms and library is either fast or storage efficient and xdrfile is storage efficient but slow. Our aim was to combine speed and storage efficiency through the xdrfile’s code modification. Here we present libxtc, a ready-to-use library for reading MD trajectory files in xtc format. The effectiveness of libxtc is demonstrated for several biomolecular systems of various sizes (~ 2 × 104 to ~ 2 × 105 atoms). In sequential mode, the performance of libxtc is up to 1.8 times higher and 1.4 times lower than xdrfile and tng, respectively. In parallel mode, libxtc is about 3 and 1.3 times faster than xdrfile and tng. At the same time, MD data stored in the xtc format require about 1.3 times less disk space than those treated with the tng algorithm in the fastest reading mode, which is a noticeable saving especially when the MD trajectory is long and the number of atoms is large—this applies to most biologically relevant systems. The online version contains supplementary material available at 10.1186/s13104-021-05536-5.
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