gmx mdmat makes distance matrices consisting of the smallest distance between residue pairs. With -frames , these distance matrices can be stored in order to see differences in tertiary structure as a function of time.

GROMACS 本身有一个命令 mdmat 可以计算残基接触图。 例如： -mean 输出的是时间平均后的残基接触矩阵， -frames 则是逐帧的残基接触矩阵， -no 参数还会输出接触的数量等信息。 -nlevels 可以控制层级数量，比如说上面的命令就可以控制数据精度在0.001，默认的层级数量是40。 -t 的含义则是截断距离，默认是1.5 nm。 运行命令之后会要求选择计算的组，可以根据自己需要进行选择。 mdmat 命令默认计算的是残基对之间的最短距离，也即如果选择的是 Protein …

gmx mdmat makes distance matrices consisting of the smallest distance between residue pairs. With -frames , these distance matrices can be stored in order to see differences in tertiary structure as a function of time.

gmx mdmat makes distance matrices consisting of the smallest distance between residue pairs. With -frames , these distance matrices can be stored in order to see differences in tertiary structure as a function of time.

Oct 31, 2022 · 本文介绍了残基接触图在蛋白质动力学研究中的重要性，它能揭示蛋白质结构信息和动态变化。通过GROMACS的gmx mdmat命令和ConAn工具，详细分析了逐帧残基接触矩阵、总接触时间矩阵、Pearson相关矩阵等多个方面，展示了残基距离在蛋白质结构分析中的应用。

I want to investigate contacts between residues in chain A and chain B during MD simulation. I am not sure how to use gmx mdmat program as it chooses only a single group from index file.

gmx mdmat makes distance matrices consisting of the smallest distance between residue pairs. With -frames , these distance matrices can be stored in order to see differences in tertiary structure as a function of time.

gmx mdmat makes distance matrices consisting of the smallest distance between residue pairs. With -frames , these distance matrices can be stored in order to see differences in tertiary structure as a function of time.

gmx-mdmat(1) man page. gmx mdmat makes distance matrices consisting of the smallest distance between residue pairs. With -frames, these distance matrices can …

GROMACS is a full-featured suite of programs to perform molecular dynamics simulations, i.e., to simulate the behavior of systems with hundreds to millions of particles using Newtonian equations of motion.