When I run a simulation (md) with hydrogen peroxide, and then view the
resulting structure in vmd I get a dihedral angle through all the atoms
(sequentially H-O-O-H) I get a value of 4.92, I also got the same value
using ghemical. However, when I run g_angle I can't seem to match that
value. I have tried putting all possible combinations of the atoms in my
index file and running with -all but the closest value was 8.877. Is is
possible I'm misunderstanding how g_angle works, if you need more
information/files from me please let me know.
command I used to run g_angle:
g_angle_d -f h2o2_em.trr -s h2o2_em.tpr -n tryangle.ndx -type dihedral -ov
test.xvg -all
Thank you for your time and any assistance you can provide
fiske
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