Hello everyone!

Warm greetings!

I have a trajectory from CG simulation of a small protein in replicas well separated and kept in the box to check if chains aggregate through time. I want a distance matrix through trajectory analysis to evaluate distances between paired protein molecules, such that i get the distance between all possible molecules and for each frame. What should be additional flags to compute this distance matrix. I have already indexed all the protein chains using the atom number using the GRO file.

Thanks in advance.

Pratibha