[gmx-users] Regarding inter helical distance using g_bundle

[bipin singh]

Hello,

I want to calculate inter helical distance between two helices using
g_bundle. As mentioned in the manual that
"g_bundle reads two index groups and divides both of them in -na
parts. The centers of mass of these parts define
the tops and bottoms of the axes".
Please suggest me out of two possible options given below which one is
the correct way of defining two index groups for calculating
inter helical distance :

(1) Atom1(CA) and Atom3(CA) in one index and Atom2 and Atom4 in another index
(2) Atom1(CA) and Atom2(CA) in one index and Atom3 and Atom4 in another index


For reference I am sending the link of figure with above Atom labels.

http://researchweb.iiit.ac.in/~bipin.singh/helix.html

Please have a look at the figure and provide your suggestions.


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Regards,
Bipin Singh