Dien Hung, Deane Charlotte M, Knapp Bernhard
Department of Analysis and Scientific Computing, Vienna University of Technology, Vienna, 1040, Austria.
J Comput Chem. 2014 Jul 30;35(20):1528-31. doi: 10.1002/jcc.23650. Epub 2014 Jun 12.
Molecular dynamics (MD) simulations are a state-of-the-art computational method used to investigate molecular interactions at atomic scale. Interaction processes out of experimental reach can be monitored using MD software, such as Gromacs. Here, we present the gro2mat package that allows fast and easy access to Gromacs output files from Matlab. Gro2mat enables direct parsing of the most common Gromacs output formats including the binary xtc-format. No openly available Matlab parser currently exists for this format. The xtc reader is orders of magnitudes faster than other available pdb/ascii workarounds. Gro2mat is especially useful for scientists with an interest in quick prototyping of new mathematical and statistical approaches for Gromacs trajectory analyses. © 2014 Wiley Periodicals, Inc.
分子动力学（MD）模拟是一种用于在原子尺度上研究分子相互作用的先进计算方法。超出实验范围的相互作用过程可以使用MD软件（如Gromacs）进行监测。在这里，我们展示了gro2mat软件包，它允许从Matlab快速轻松地访问Gromacs输出文件。Gro2mat能够直接解析最常见的Gromacs输出格式，包括二进制xtc格式。目前没有公开可用的Matlab解析器用于这种格式。xtc读取器比其他可用的pdb/ASCII变通方法快几个数量级。Gro2mat对于有兴趣为Gromacs轨迹分析快速开发新的数学和统计方法的科学家特别有用。© 2014威利期刊公司。
