I have 100 ns trajectory of a protein-protein complex generated using GROMACS. I wanted to calculate the angle between 2 chains but before that I wanted to fix 1 chain so that it is not moving but the other chain is moving. How can I do that?
I have used gmx trjconv -fit rot+trans but still i can see some movement in the protein that is fixed. I want it to be absolutely static so that the change in angle values over trajectory only comes from the movement of the chain that is moving..