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
--
========================================
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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