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Thanks for the suggestion.<br>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? <br>Thanks a lot for your help.<br>Best wishes,<br>Rebeca.<br><br>> Date: Thu, 16 Dec 2010 11:59:38 -0500<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] g_bundle question<br>> <br>> <br>> <br>> Rebeca García Fandiño wrote:<br>> > Hello,<br>> > I am trying to calculate the tilt angle of the principal axis of a <br>> > nanotube inserted into a membrane using g_bundle. In the index file I <br>> > have selected a group of atoms at the top and a group of atoms at the <br>> > bottom of the nanotube, and I using the option -na 1 and -z to calculate <br>> > the tilt respect to the z axis of the membrane.<br>> > I suppose that the results I have obtained in bun_tilt.xvg are the tilt <br>> > angles respect to the average axis (along the simulation), is that <br>> > right? Is there any way to calculate the tilt angle respect to a <br>> > reference axis (for example, the axis formed by the 2 groups in the <br>> > index file in the first structure, which is just perpendicular to the <br>> > membrane?<br>> <br>> Sounds like something g_sgangle can do.<br>> <br>> -Justin<br>> <br>> > Thanks a lot in advance for your help.<br>> > Best wishes,<br>> > <br>> > Rebeca Garcia<br>> > Santiago de Compostela University<br>> > Spain<br>> > regafan@hotmail.com<br>> > <br>> <br>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> MILES-IGERT Trainee<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> <br>> ========================================<br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br> </body>
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