I did polypeptide MD simulation of two protein sequences by GROMACS. The difference between both sequences is only position of residue, we change position of Histidine residue from 1st position to 3rd position. By doing this we are observing difference in non bonded Columb energy for two sequences. Once we further divide the sequence into two half parts, and again calculate columb interaction energy, we observed that the difference is coming from the first half parts rest of the parts energy is same for both sequences… now i did clustering of trajectory and extracted 10 frames from first 10 cluster…now how can I observed the structural difference between these frames which explains why change of position of Histidine from 1st to 3rd place in sequence lead to difference in columb energy . The LJ part of energy is same In the entire comparable for both sequences.