[gmx-users] Regarding inter helical distance using g_bundle

Gianluca Santoni gianluca.santoni at ibs.fr
Tue Nov 29 15:03:26 CET 2011

On 11/29/11 2:10 PM, 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.
> -----------------------
> Regards,
> Bipin Singh
I think g_dist is a easier choice.

Gianluca Santoni,
Institut de Biologie Structurale
41 rue Horowitz
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