Dear GMX users, I would like to calculate the angle of a transmembrane helix long axis with respect to the membrane normal and see how this angle fluctuates during the simulation.
In the forums, people were suggesting to use gmx helixorient. I used it with the following command: gmx helixorient -f trajectory.trr -s md.tpr -n index.ndx -otilt tilt_TM1CA.xvg and I choose the c-alpha of one transmembrane helix from the index file. When I plotted the results of -otilt I obtained a weird graph with an angle equal to 0 during the entire simulation and this is not what I see when I visualize it. I am not sure if I am using the tool in the correct way or if it is the right tool to use. If yes, how can gmx helixorient detect the membrane normal? and how can I interpret the results? I would really appreciate if someone can help me with this. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
