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

[Dallas Warren]

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, then generate an index
group for each specific dihedral of four atoms and then process using gmx
angle -ov

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Tue, 25 Feb 2020 at 10:55, Sadaf Rani <sadafrani6 at gmail.com> wrote:

> 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
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