[gmx-users] g_bundle to calculate angle with z-axis

Sarah Witzke sawit02 at student.sdu.dk
Sun Nov 8 20:49:34 CET 2009

Dear gromacs users,


I am conducting an analysis on my system consisting of a DMPC bilayer with small organic molecules inserting into it. The small molecule consists of a ring with two substituents opposite each other (like para for a benzene ring). Below I have tried to sketch the ring of the molecule with the two 'para' substituents: 



                    /  \                  

                   |     |

                    \  /



I want to create a vector starting in '1' and having the arrow head in '2' and then calculate how the angle between this vector and the z-axis varies during the simulation.  

To do this I created an .ndx file consisting of two groups, namely the atom '1' and the atom '2'. Afterwards I used g_bundle (version 4.0.4 since my simulations are done in this version):

g_bundle -f xxx.xtc -s xxx.tpr -n xxx.ndx -na 1 -z -ot xxx.xvg

When asked for two groups I first give group 0 corresponding to atom '1' and the I give group 1 corresponding to atom '2'. 

The result is rotated 180 degrees from what I would expect from looking at the simulation. Am I giving the groups in the wrong order? Will the order used correspond to a vector starting in '2' and with arrow head in '1'?

By the way, is 1 the correct value for -na in this situation? I find it a bit difficult to understand that paragraph of the manual.


Thank you, 


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