[gmx-users] g_angle dihedrals

[Robert fiske]

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

_________________________________________________________________
More photos, more messages, more storage—get 2GB with Windows Live Hotmail. 
http://imagine-windowslive.com/hotmail/?locale=en-us&ocid=TXT_TAGHM_migration_HM_mini_2G_0507