[gmx-users] How to calculate the dihedral angle as a function of time?

[Sadaf Rani]

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 options, How can I identify these groups show which
part of the system. I want to calculate the dihedral angle as a function of
time in the simulation.

Group     0 ( Phi=0.0_3_0.65) has   228 elements
Group     1 ( Phi=0.0_1_0.84) has     8 elements
Group     2 ( Phi=0.0_2_0.84) has     8 elements
Group     3 ( Phi=0.0_3_1.67) has    16 elements
Group     4 ( Phi=0.0_3_0.67) has    52 elements
Group     5 ( Phi=0.0_1_1.05) has    96 elements
Group     6 ( Phi=0.0_3_0.70) has     4 elements
Group     7 (Phi=180.0_2_10.46) has    32 elements
Group     8 ( Phi=0.0_1_8.37) has    16 elements
Group     9 ( Phi=0.0_2_8.37) has     8 elements
Group    10 ( Phi=0.0_2_1.13) has     8 elements
Group    11 ( Phi=0.0_3_1.76) has     8 elements
Group    12 (Phi=180.0_1_1.88) has     4 elements
Group    13 (Phi=180.0_2_6.61) has     4 elements
Group    14 (Phi=180.0_3_2.30) has     4 elements
Group    15 ( Phi=0.0_1_3.35) has     4 elements
Group    16 (Phi=180.0_3_0.33) has     4 elements
Group    17 (Phi=180.0_2_15.17) has    96 elements
Group    18 ( Phi=0.0_3_0.75) has     8 elements
Group    19 (Phi=180.0_2_1.05) has    20 elements
Group    20 (Phi=180.0_1_0.84) has    20 elements
Group    21 ( Phi=0.0_3_0.63) has    32 elements
Group    22 ( Phi=0.0_2_3.35) has    12 elements
Group    23 ( Phi=0.0_3_0.67) has    28 elements
Group    24 ( Phi=0.0_3_0.70) has    20 elements
Group    25 ( Phi=0.0_3_0.60) has    24 elements
Group    26 ( Phi=0.0_2_4.92) has    24 elements
Group    27 ( Phi=0.0_3_0.65) has    96 elements
Group    28 ( Phi=0.0_3_1.60) has    24 elements
Group    29 ( Phi=0.0_3_1.60) has    12 elements
Group    30 (Phi=180.0_2_0.42) has    12 elements
Group    31 ( Phi=0.0_3_0.75) has    12 elements

I tried gmx chi also by the following command:-

gmx chi -s md.gro -f md.xtc -all 1 -o dihedral.xvg
The out put file indicate following information
 xaxis  label "Residue"
 yaxis  label "S2"
What is S2 on y-axis.
How should I interpret it? Could anyone please help me with this? I would
really appreciate your kind suggestions.

Thanks.
Sadaf