Department of Theoretical Physics and Swedish e-Science Research Center, Royal Institute of Technology, Science for Life Laboratory, Box 1031, SE-171 21, Solna, Sweden.
J Comput Chem. 2014 Jan 30;35(3):260-9. doi: 10.1002/jcc.23495. Epub 2013 Nov 20.
Molecular dynamics simulations is an important application in theoretical chemistry, and with the large high-performance computing resources available today the programs also generate huge amounts of output data. In particular in life sciences, with complex biomolecules such as proteins, simulation projects regularly deal with several terabytes of data. Apart from the need for more cost-efficient storage, it is increasingly important to be able to archive data, secure the integrity against disk or file transfer errors, to provide rapid access, and facilitate exchange of data through open interfaces. There is already a whole range of different formats used, but few if any of them (including our previous ones) fulfill all these goals. To address these shortcomings, we present "Trajectory Next Generation" (TNG)--a flexible but highly optimized and efficient file format designed with interoperability in mind. TNG both provides state-of-the-art multiframe compression as well as a container framework that will make it possible to extend it with new compression algorithms without modifications in programs using it. TNG will be the new file format in the next major release of the GROMACS package, but it has been implemented as a separate library and API with liberal licensing to enable wide adoption both in academic and commercial codes.
分子动力学模拟是理论化学中的一个重要应用，而随着当今大型高性能计算资源的可用性，这些程序也会生成大量的输出数据。特别是在生命科学领域，对于复杂的生物分子如蛋白质，模拟项目通常需要处理数太字节的数据。除了需要更具成本效益的存储外，能够归档数据、确保数据在磁盘或文件传输错误方面的完整性、提供快速访问以及通过开放接口促进数据交换也变得越来越重要。已经有了各种各样不同的格式，但很少有（如果有的话）格式能够满足所有这些目标。为了解决这些缺点，我们提出了“轨迹下一代”（TNG）——一种灵活但高度优化和高效的文件格式，旨在考虑互操作性。TNG 既提供了最先进的多帧压缩，又提供了一个容器框架，这将使得可以在使用它的程序中不进行修改的情况下，用新的压缩算法对其进行扩展。TNG 将成为 GROMACS 软件包的下一个主要版本中的新文件格式，但它已作为一个单独的库和 API 实现，采用了宽松的许可，以便在学术和商业代码中广泛采用。
