DR LIDIYA!! Distance Matrix calculation — MDAnalysis.analysis.ensemble.confdistmatrix ¶. The module contains a base class to easily compute, using parallelization and ...

https://www.mdanalysis.org/docs/documentation_pages/analysis/encore/confdistmatrix.html

https://www.researchgate.net/post/How_to_calculate_PBC_box_size_while_doing_protein_unfolding_MD_simulation

Regards--

Hey Lidiya! Since I do not know what MD code you are using and MDAnalysis can take trajectories produced in different formats I could recommend you to use tools from either Gromacs or MDynaMix. MDynaMix can take xmol and pdb pretty well (but you shall check the manual about how to write your input-file). Gromacs can analyze xtc, pdb and gro formats. Both codes take care of pbc. However, for Gromacs you might need to create a "dummy" tpr-file in order to proceed with the routine. I am not sure why would you see distances between groups, because then you will get only average values which might not appear to you or to the one who will read your work in a clear way. If you are interested in distances between groups then perhaps calculating RDFs would more suitable thing to do.

Thank you for the answers. I use Gromacs output files (.tpr for topology and .xtc for trajectory). I want to follow the change in distance between two objects within some period of time, so there is no problem that the function would calculate the average distance. Moreover, the problem could be reduced to calculation of distance between two center of mass/geometry. Yet the box parameters and the fact that periodic boundary conditions are applied should be taken in count.