[gmx-users] g_helixorient

[Sudera, Prerna (INT)]

Hello,

I have been working with some dimer protein molecule, on gromacs, trying to analyze the structure of the dimer, and how the monomers orient according to eachother. The monomer is an alpha-helix, having 36 residues.
I wanted to calculate the rho angle for some residues in my helical protein, which is related to the rotation of the helix, after it is tilted from the normal membrane. I have been using the gromacs tool g_helixorient, in a hope to figure the out the rho angle. However, the description for this tool, as provided in the manual is very insufficient, and i have no idea what the output files mean. I get a list of output files, namely:

helixorient.dat
center.dat
theta1.xvg
theta2.xvg
theta3.xvg
tilt.xvg
rise.xvg
rotation.xvg
radius.xvg

I wanted to get access to a source, which could help in clearly assessing these files. I have been unable to understand anything from the code file, as i am very new to simulation and coding. I would be very grateful, if some sort of help in understanding this tool better, could be given.

Best wishes,
Prerna?