[gmx-users] Measure angle with g_sgangle

[Mast, Thilo]

Hey.
I'm using Gromacs to simulate a transmembrane-peptide and would like to measure the angle between three residues of the protein. The protein gets during the simulation a kink of about 87°. I would like to measure the real angle of the kink with g_sgangle.
So I made an index file and defined two groups with:

a 5|a 248
name 17 group1

and

a 248|a 477
name 18 group2

The atom numbers are the C alpha atom of the N terminus, the AS where the kink is located and the C terminus.

Now I used g_sgangle to measure the angle between this two groups with:

g_sgangle -f md_27nstrjconv.trr -n g_sgangle.ndx -s md_27ns.tpr -oa sg_angle.xvg

Then I've chosen group1 and group2 (17 18).
The sg_angle.xvg looks like that:

@    title "Angle between group1 and group2"
@    xaxis  label "Time (ps)"
@    yaxis  label "Angle (degrees)"
@TYPE xy
           0      0.200158       78.4538
          10      0.224148       77.0472
          20       0.25729       75.0907
          30      0.237989       76.2321
          40      0.250923       75.4679
          50      0.232999       76.5263
          60      0.267666       74.4746
          70      0.227826       76.8309
          80      0.286902       73.3274
          90      0.250226       75.5091
         100      0.254623       75.2488
...

So it tells me that Gromacs measured an angle of about 0.2??!
Can anyone tell me what I am doing wrong? And what tells me the third column of the .xvg file?

Thilo