How to choose the correct options for the gmx distance analysis?

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,

So I’m not sure if this late reply is still useful, but to me, the graphs only look the same on average, but definitely have peaks occurring on different spots. If you want to double check, you could also try making the same distance graph using VMD for the distance between the 2 atoms. Once you load your .gro and .xtc file into the program, go to Mouse > Label > Bonds to then select the 2 atoms, then Graphics > Labels and you should be able to output a graph of the distance between the 2 atoms.

Hope this helps!