Dear gromacs users, I want to calculate NH vector for my ligand simulations using g_rotacf. I want to ask if I first need to remove rotation and translation degrees of freedom from the trajectory using the command: trjconv -f traj.xtc -s 10nsProd_MD.tpr -fit rot+trans -o no_rot_trans.xtc
Also, when I am using this command which group I should select for least square fit (ligand or the whole system) and a group for output. The rotation correlation functions (g_rotacf) output depends on trajectory type which I have. So C(t) graphics are different if I remove rotation and translation degrees of freedom. Please can you advice me on this? Yours sincerely, Olga
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