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OK,<br>you are right, I haven´t noticed the -z option! <br>I will try it.<br>Thanks a lot for your help.<br>Best wishes,<br>Rebeca.<br><br>> Date: Thu, 16 Dec 2010 15:34:05 -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>> > Thanks for the suggestion.<br>> > However, I have one question. If I use g_sgangle I can calculate the <br>> > angle formed by the atoms at the top and bottom of my nanotube, but if <br>> > the nanotube is considered as a whole (as a rigid system), and it tilts, <br>> > then the result would not show the tilt respect to the z axis of the <br>> > membrane, am I right?<br>> <br>> Maybe I'm not clear on what you want. I haven't used g_sgangle much, but it <br>> seems to me that option -oa ("Angle between the two groups specified in the <br>> index file") would do what you want. Otherwise, g_sgangle -z might.<br>> <br>> -Justin<br>> <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 <br>> > 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 <br>> > 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 <br>> > 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>> <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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