GROMACS modification: No
I am simulating two carbohydrate chains with box length of 59 Angstrom. The distance between two atoms (picked from two different carbohydrate polymers) are calculated using MDAnalysis (I have also verified with VMD). The distance varies with time as follows:
Clearly one can observe distance between two atoms exceeds the box length at some time frames.Here I have also attached snapshot of 990th frame and pointed out the two atoms.
At this particular frame the distance between two atoms is 81.17 Angstrom.
**The frame was corrected using trjconv with pbc mol and center flag.
Please let me know if I can provide any further information and please do comment on any technical or conceptual point I am missing here. That would be really great!! :)