[gmx-users] Principal axis (g_principal)

Sarah Witzke sawit02 at student.sdu.dk
Sun Dec 20 13:20:19 CET 2009

Dear gmx users,

I am doing several analyses (version 4.0.4) on my simulations with small organic molecules inserting into a DMPC bilayer. Now I would like to calculate whether the small molecule inserts into the membrane with a specific angle to the membrane normal (or z-axis). I have used two approaches:

1) My molecule is a cyclohexene ring with two "para" substituents. I made an index group with carbon number 3 and number 10 (in different groups) which corresponds to the first substituent-atoms on each side of the ring. This vector describes the shape of the molecule quite well. I then used g_bundle to calculate the angle between this vector and the z-axis by echoing first the C3-group and then the C10-group:

echo 0 1 | g_bundle -f xxx.xtc -s xxx.tpr -n xxx-vector.ndx -na 1 -z -ot xxx-vector.xvg

This gives fairly reasonable results and angle distribution.

2) I also calculated the principal axis by g_principal where I echoed each small molecule as a whole:

echo 0 | g_principal -f xxx.xtc -s xxx-1.tpr -n xxx-lim.ndx -a1 xxx-principal.dat -a2 xxx-axis2.dat -a3 xxx-axis3.dat

To get the angle between the principal axis and the z-axis one takes the arcos the the z-component. This created quite a different and very broad angle distribution.


This puzzled me very much since the difference between the C3-C10 vector and the principal axis should not be that great.

I then used a small python program to calculate the principal axis of my molecule and the result was again quite different than from g_principal. I have tried to rotate each of my substituent groups by 120 degrees (creating 9 different conformations) and then calculate the difference in the principal axis but this creates only a deviation of max. 16-17 degrees not at all accounting for the very different angle distributions seen. I have not included numbers but I can do so along with the python code. I would like to ask if anyone can see any obvious mistakes or know of something special to be aware of when using g_principal?


Thank you,


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