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: [email protected] 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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