GROMACS modification: Yes/No
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I want to plot “the distance between a pair of benzene (only C-atoms) centroids vs time” for the MD run.
I found that gmx traj can be used to extract the centre of mass of these benzene rings using index. The system has a total of 12 pairs of such benzene rings. So, extracting 24 centroids separately and calculating distances between them followed by plotting them seems to be very tedious.
Is there any way to use gmx to extract all centroids in one go (as gmx angle, pairdist, etc.)? Or is there any other script to extract such kind of data?
Thank you for your time.