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

anna_gromacs at libero.it anna_gromacs at libero.it
Tue May 14 16:25:39 CEST 2013

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...


More information about the gromacs.org_gmx-users mailing list