[gmx-users] Using -all flag in g_angle command

GAYATHRI S gayathri.s at iitb.ac.in
Wed Jan 14 07:21:50 CET 2015

Hello everyone,

I simulated an NADH molecule. I want to check how each of the dihedral
angles changes during the simulation. In other words, I want to plot a
graph of individual (not average) dihedral angles versus time.

To do so, I created an index file using the following command:

$ mk_angndx -s full.tpr -n angle.ndx -type dihedral

Next, I used the g_angle command as follows:

$ g_angle -f full.xtc -n angle.ndx -type dihedral -all

However, this command generated only one output file angdist.xvg. The -ov
flag generates angles in degrees; but, it gives values in average and I
want the same plot for individual angles.

Please suggest how to proceed.

Thank you.

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