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

anna_gromacs at libero.it anna_gromacs at libero.it
Tue May 14 14:38:03 CEST 2013

Dear users and experts, 

my question is about the results given by the program g_sgangle, 
when I try to calculate the angles between the two vectors defined by 3 consecutive P atoms, on the DNA structure (a single gro structure), the result is:

@    title "Angle between a_728_695 and a_695_662"
@    xaxis  label "Time (ps)"
@    yaxis  label "Angle (degrees)"
@TYPE xy
           0      0.855195       31.2188
respectively time, angle and arccosine.

By literature is well known that  viewing down the long axis of the DNA molecule, the P atoms are around in circle, and it would be numerically possible to calculate the angle between the two vector defined by 3 consecutive P atoms. If I'm right it is: (180° - 32.3°)= 147.7. So the value given by sg_angle is too low. 
Where I'm wrong?

Many many thanks,

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