[gmx-users] g_angle dihedrals

Robert fiske rfiske_ at hotmail.com
Wed May 23 17:11:02 CEST 2007

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


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