[gmx-users] g_bundle question

[Rebeca García Fandiño]

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?
Thanks a lot in advance for your help.
Best wishes,

Rebeca Garcia
Santiago de Compostela University
Spain
regafan at hotmail.com
 		 	   		  
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