[gmx-users] Measure angle with g_sgangle

[Justin A. Lemkul]

On 5/15/12 2:47 PM, Mast, Thilo wrote:
> 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?
>

The second column is the cosine of the angle.  The third column is the actual angle.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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