OK, you are right, I haven´t noticed the -z option! I will try it. Thanks a lot for your help. Best wishes, Rebeca.
> Date: Thu, 16 Dec 2010 15:34:05 -0500 > From: [email protected] > To: [email protected] > Subject: Re: [gmx-users] g_bundle question > > > > Rebeca García Fandiño wrote: > > Thanks for the suggestion. > > However, I have one question. If I use g_sgangle I can calculate the > > angle formed by the atoms at the top and bottom of my nanotube, but if > > the nanotube is considered as a whole (as a rigid system), and it tilts, > > then the result would not show the tilt respect to the z axis of the > > membrane, am I right? > > Maybe I'm not clear on what you want. I haven't used g_sgangle much, but it > seems to me that option -oa ("Angle between the two groups specified in the > index file") would do what you want. Otherwise, g_sgangle -z might. > > -Justin > > > Thanks a lot for your help. > > Best wishes, > > Rebeca. > > > > > Date: Thu, 16 Dec 2010 11:59:38 -0500 > > > From: [email protected] > > > To: [email protected] > > > Subject: Re: [gmx-users] g_bundle question > > > > > > > > > > > > Rebeca García Fandiño wrote: > > > > Hello, > > > > I am trying to calculate the tilt angle of the principal axis of a > > > > nanotube inserted into a membrane using g_bundle. In the index file I > > > > have selected a group of atoms at the top and a group of atoms at the > > > > bottom of the nanotube, and I using the option -na 1 and -z to > > calculate > > > > the tilt respect to the z axis of the membrane. > > > > I suppose that the results I have obtained in bun_tilt.xvg are the > > tilt > > > > angles respect to the average axis (along the simulation), is that > > > > right? Is there any way to calculate the tilt angle respect to a > > > > reference axis (for example, the axis formed by the 2 groups in the > > > > index file in the first structure, which is just perpendicular to the > > > > membrane? > > > > > > Sounds like something g_sgangle can do. > > > > > > -Justin > > > > > > > Thanks a lot in advance for your help. > > > > Best wishes, > > > > > > > > Rebeca Garcia > > > > Santiago de Compostela University > > > > Spain > > > > [email protected] > > > > > > > > > > -- > > > ======================================== > > > > > > Justin A. Lemkul > > > Ph.D. Candidate > > > ICTAS Doctoral Scholar > > > MILES-IGERT Trainee > > > Department of Biochemistry > > > Virginia Tech > > > Blacksburg, VA > > > jalemkul[at]vt.edu | (540) 231-9080 > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > > > ======================================== > > > -- > > > gmx-users mailing list [email protected] > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > > Please don't post (un)subscribe requests to the list. Use the > > > www interface or send it to [email protected]. > > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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