To work out which dihedrals those index groups refer to, you will need to
look at the index numbers in each index group, then match them with those
in the coordinate file.
Do you have a specific dihedral(s) that you want to follow, or is all all
dihedrals of the same type? If specific dihedrals, t
Dear Gromacs users
I want to calculate the dihedral angle over the simulation time. I tried
following commands:-
gmx mk_angndx -s topol.tpr -type dihedral
which generates an index file for dihedral angles then running:-
gmx angle -f md_prod.trr -n angle.ndx -type dihedral
gives following group o
