> > Stefan Hoorman wrote: > > > > Stefan Hoorman wrote: > > > How can I calculate the angle between a helix inserted in a > > membrane and > > > the axis perpendicular to the surface of the membrane. I have > tried > > > using g_helixorient, but the graphs all come as a straight line > > in zero. > > > > See -z in g_sgangle -h > > > > Mark > > > > > > Thank you for the tip, but again I faced a problem. I could only analyse > > using g_sgangle with an index group containing 3 atoms. Then the problem > > is, since my helix not only tilts, but also it bends a little back and > > forth, the angle between it and the z axis will vary greatly depending > > on which three atoms I choose. I imagined that by choosing three alpha > > carbon atoms every four residues would give me a good outcome, but it > > turns out that the angle changes a lot, and I am guessing it is because > > of this bending movement. When I say "changes a lot" I mean; it starts > > at 0º and gets up to 50º, which i imagine to be a little bit too much. > > Would there be a better way to calculate this? > > g_principal will calculate the axes of inertia, from which you can > calculate the angle with the Z-axis. > > Mark > > Ok, thank you for the info, but now I got a little bit confused. What exactly does the info from axis1.dat, axis2.dat, axis3.dat and moi.dat mean? And how would I use this info to calculate the helix tilt. I know the general meaning of principal axes of inertia, but I could not find any information more specific to this type of caltulation I need to do. If you could give any reference or any other type of information a little bit more specific I would be very greatful. I mean, if it is not too much to ask. Thank you Stef.
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
