Dear all,
I was trying to calculate the angle between two protein moiety (CA759-CA6-CA205). The expected angle between moiety should be around 20-40 degree, however, I got some surprising angle using the ‘gmx angle’ tool (Please see the attached figure). When I check all the angles with VMD, the actual angles between CA759-CA6-CA205 are near about 20-40 degrees. For a particular time, e.g., 455340 ps, the calculated angle with ‘gmx angle’ tool is 135.693, however, the actual should be around 17 degree!

I did convert the MD trajectory file and then calculated angle using the following commands

Dear Dr. DBW,
Thank you very much for your reply and suggestion. I tried with ‘-pbc whole’ as well as ‘-pbc mol -center’ options along with ‘-pbc mol -ur compact’, however, I got the same results. FYI, the calculated RMSD or Rg didn’t show any problem. I visualize the trajectory using VMD and didn’t notice any broken fragment. And the observed angle is around 20-40 degree.

Only other suggestion I have is that you check the trajectory at the times exactly when it does the jump up to 150. And measure the angle at various time points using VMD and check those against the values found using the gmx script.

Hey Kalyan,
I would suggest you look into the index that you have defined. What it looks like to me is that gmx angle is giving you the 180 - angle, as your expectation is within 20-40 deg and the plot shows values from 130-170.