GROMACS version: 2019.4
Hi gromacs users. I did md simulation of my system containing 1 polymer and 1 drug molecule. I want to know what the distance between the two (polymer and drug) is during the simulation time. To this aim, I used:
gmx_mpi distance -f final.xtc -s md.tpr -n index.ndx -oav dist_com.xvg -select ‘com of group 2 plus com of group 3’
group 2: polymer
group 3: drug
Since the polymer sometimes folds during the simulation time and sometimes becomes linear, also, I used the following command to investigate the distance between two especial atoms of polymer molecule (group 8: O atom) and drug molecule (group 9: N atom).
gmx_mpi distance -f final.xtc -s md.tpr -n index.ndx -oav dist_atom.xvg -select ‘atom of group 8 plus atom of group 9’
The surprising thing for me is that the graphs of both analyzes are exactly the same. Is this correct or should I do something special?
Please check the image sent.
Best,