Title: Mxdrfile: read and write Gromacs trajectories with Matlab Show Chinese title

Title: Mxdrfile: 使用 Matlab 读写 Gromacs 轨迹

Abstract: Progress in hardware, algorithms, and force fields are pushing the scope of molecular dynamics (MD) simulations towards the length- and time scales of complex biochemical processes. This creates a need for developing advanced analysis methods tailored to the specific questions at hand. We present mxdrfile, a set of fast routines for manipulating the binary xtc and trr trajectory files formats of Gromacs, one of the most commonly used MD codes, with Matlab, a powerful and versatile language for scientific computing. The unique ability to both read and write binary trajectory files makes it possible to leverage the broad capabilities of Matlab to speed up and simplify the development of complex analysis and visualization methods. We illustrate these possibilities by implementing an alignment method for buckled surfaces, and use it to briefly dissect the curvature-dependent composition of a buckled lipid bilayer. The mxdrfile package, including the buckling example, is available as open source at http://kaplajon.github.io/mxdrfile/ . Show Chinese abstract

Abstract: 硬件、算法和力场的进步正在将分子动力学(MD)模拟的范围推向复杂生化过程的长度和时间尺度。 这需要开发针对当前特定问题的高级分析方法。 我们介绍了mxdrfile，这是一个用于操作Gromacs二进制xtc和trr轨迹文件格式的快速例程集合，Gromacs是最常用的MD代码之一，而Matlab是一种强大的科学计算语言。 能够同时读取和写入二进制轨迹文件的独特功能，使得可以利用Matlab的广泛功能来加快并简化复杂分析和可视化方法的开发。 我们通过实现一种用于弯曲表面的对齐方法，并用它简要分析了弯曲脂质双层的曲率依赖组成来说明这些可能性。 mxdrfile软件包，包括弯曲示例，可在http://kaplajon.github.io/mxdrfile/ 免费获取。