[gmx-users] g_sgangle and P atoms on the DNA molecule.

[Justin Lemkul]

On 5/14/13 10:25 AM, anna_gromacs at libero.it wrote:
> Dear all,
> in referring to the described probelm with g_sgagle results, I would like to add the following:
> I made an index file like this:
>
> 0 System              :   762 atoms
> 1 DNA                 :   762 atoms
> 2 a_412_444           :     2 atoms
> 3 a_444_474           :     2 atoms
>
> with:g_sgangle -f box.gro -n index.ndx -s topol.tprI calculated the angle between the gruop 2 and 3. I obtained the value:
> @    title "Angle between a_412_444 and a_444_474"
> @    xaxis  label "Time (ps)"
> @    yaxis  label "Angle (degrees)"
> @TYPE xy
>             0      0.883076       27.9844
> But the same angle calculate simply putting the label with VMD program is 152.016.
> I think there is something that is not so clear...

180 - 152.016 = 27.984.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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