I want to measure the tilt of helix with the normal of bilayer. My system is basically a dimer with two helices. Since using sidechain atom relative to the axis is optional, I simply defined the index file of C-alpha atoms of these two helices and measured the time evolution of tilt angle.
Since it is a dimer system, I don't know how gmx helixorient defines the helical axis and the axis of bilayer. The basic command I've used for this is:
gmx helixorient -s NPT_mut_0_eq.tpr -f mutant_nopbc.trr -n helix.ndx -b 100000 -e 150000 -oaxis -ocenter -orise -oradius -otwist -obending -otilt -orot
Hi Roshan,
I would recommend treating each peptide in the dimer as a separate system to measure the tilt angle of. Imagine a dimer, with one peptide tilted at 30deg relative to the bilayer normal, and the other peptide tilted at 15deg. The gromacs tool will probably generate a vector relative to both peptides in the dimer, thus not yielding either 30 deg or 15 deg but something in between.
When plotting your results, don't be afraid to make multiple graphs e.g., multiplot in GNUPLOT. If you have two systems (two dimers), then you would have two graphs (one wildtype and the other mutant) and helixA and helixB in each.
Hope that helps :-)
Hi, our software can easily detect the axis of your dimer. Please give it a try, https://team.inria.fr/nano-d/software/ananas/.
Then, use the detected axis to compute the angle with the z-axis of your bilayer (I suppose it's along z because of PBC).
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