GROMACS version: 2019.5
GROMACS modification: Yes
I am working with a six residue protein and I was computing the dihedral angles using the tool gmx chi with the flag -rama. Thus, I can see the phi and psi angles in the files called ramaPhiPsiResidue.
For residues 2, 3, 4 and 5 everything looks OK and the results are consistent with those obtained with the tool gmx rama.
On the other hand, for the residues 1 and 6 there is something I do not understand: I was expecting to obtain a column of zeros for phi in the residue 1 and a column of zeros for psi in the residue 6 (or other way round). However, these are not the cases. I am obtaining ramaPhiPsiResidue files full of angles for all frames. For those two residues, what do those angles mean?