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Conceptual representation of a transit station at the Kendall Parkway. Actual design to be provided at design phase. The Kendall Parkway is a new north-south multimodal transportation corridor west of SW 167th Avenue from the current termini of …

2017年12月10日 · 比如如果在模拟过程中，只要这个小分子与某个残基的最近距离小于某个值就当成contact，可以用gmx自带的mindist命令考察，看有多少帧处于contact状态，除以帧数就是和这个残基的contact概率。

2023年10月25日 · 大家好，最近在做关于水的二维密度分布图，通过gmx densmap 命令得到了densmap.dat文件和densmap.xpm文件，但是不知道如何绘制出如图222展示的效果，附上所得.dat和.xpm文件，谢谢大家。

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 …

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