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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
