Problems with g_dist?

12 December 2018 1 5K Report

Hi,

my system contains 30 same molecule around nanotube. each molecule is in 2nm far from nanotube. i want to know how this distance change during simulation time. I have attached the same analysis in articles. but in my case after g_dist (GROMACS), all distances are around 0.6 nm which it is not possible at least for the first step of simulation because they are in about 2nm.

Would you please help me?

Ramin Ekhteiari Salmas

It's a time dependent distance analysis - you can do it easily in VMD if you import your MD traj. into it or even by the code that you used for MD. With a little query in these mostly used programs you can do all post-processing analysis on your MD traj. frames.

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