[gmx-users] g_sgangle not working as expected

[Scott Classen]

Hello GROMACers,
I am trying to monitor a specific dihedral angle as a function of time 
in my MD simulation.
I have the following atoms for example.

A-B-C-D

I have tried doing this by defining 2 vectors in my custom index.ndx 
file
[vec1]
B A
[vec2]
C D

I have also tried defining two planes such as this:
[vec1]
C B A
[vec2]
B C D

Either way when I run g_sgangle I am only asked to select one group and 
the program appears to do some sort of self??? analysis.
Am I doing something wrong?

Here is a snippet of the output:

Reading file icrf187-water-md.tpr, VERSION 3.2.1 (single precision)
Group     0 (        vec1) has     3 elements
Group     1 (        vec2) has     3 elements
Select a group: 0 1
Selected 0: 'vec1'

Group vec1 contains the following atoms:
Atomname 0: CAI
Atomname 1: N
Atomname 2: CAO

Group vec1 contains the following atoms:
Atomname 0: CAI
Atomname 1: N
Atomname 2: CAO

Careful: distance only makes sense in some situations.

Reading frame       0 time    0.000

Last frame        100 time  100.000



~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   Scott Classen, Ph.D.
   ACS Postdoctoral Fellow
   Department of Molecular & Cell Biology
   University of California, Berkeley
   237 Hildebrand Hall #3206
   Berkeley, CA 94720-3206
   LAB 510.643.9491
   FAX 510.643.9290
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~