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

[Sarah Witzke]

By the way, I did try to choose the groups in the opposite order - i.e. first select atom '2' and then '1'. The result is a reflection in the bilayer plane - and thereby the expected result. I just wanted to be sure, that what I am doing is correct, and that it is not just coincidence that swopping the groups gives the 'wanted' result. To me it seems logic that the vector created would start in the first selected atom and have the arrow head in the second atom, but perhaps I'm just wrong ;-)

By the way the structure of the molecule should have looked like this:

                2
                |
               /  \                 
              |     |

               \  /

                |
               1  

Best, 

Sarah


________________________________

Fra: gmx-users-bounces at gromacs.org på vegne af Sarah Witzke
Sendt: sø 08-11-2009 20:49
Til: Discussion list for GROMACS users
Emne: [gmx-users] g_bundle to calculate angle with z-axis



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:

                     2

|

                    /  \                 

                   |     |

                    \  /

                      |

                     1

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,

Sarah

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