GROMACS modification: No
I have run a md simulation of protein conjugated with fluorophore,now to analyse FRET efficiency gmx dyecouple does not distinguishes donor and acceptor groups from the index.
What could be the possible solution.
Do I need to make corrections in mdp file for such simulations.
One of the requirement for gmx dyecoupl is that the dyes have to be whole in traj file. To achieve that you can use of gmx trjconv with pbc option res and mol. I am not aware of special requirement in mdp files.
What error do you get?
Thank you Alessandra
by mistake I had put same atom groups in index file, that led to this error showing both are similar and make no sense.
Extremely sorry for bothering the community for a silly mistake that I made.