[gmx-users] Regarding inter helical distance using g_bundle

Justin A. Lemkul jalemkul at vt.edu
Tue Nov 29 14:13:42 CET 2011

bipin singh wrote:
> 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.

Wouldn't it be easier to simply use g_dist to calculate the distance?



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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