[gmx-users] Creation of an index file with seperate lipid leaflets

Stéphane Téletchéa steletch at jouy.inra.fr
Wed Nov 8 18:03:58 CET 2006

Alan Dodd a écrit :
> Has anyone already created a way to generate an index
> file with the atoms from the two leaflets of a bilayer
> listed seperately?  I can't believe it hasn't already
> been done, but can't find a direct description of a
> solution.  I'm attempting a modification to make_ndx,
> (or perhaps something considerably less ambitious,
> judging by the way it's going so far) to permit lipid
> selection based on headgroup orientation, though I'd
> quite like to save myself the effort.
> Incidentally, splitres and splitat seem to be the
> wrong way around, unless I'm misunderstanding them -
> they do the opposite of what they say.  From the
> gromacs 3.3.1 source download I did on April of this
> year.
> Alan Dodd
> University of Bristol

Inflategro, written by D. Tieleman and available at:

allows easily to discriminate between upper and lower leaflet.
This is not the program's goal, but if i were to start something, i 
would definively start looking at his program (in perl). With minor 
modifications (mostly removing unuseful code for you and creating the 
output index file), i think you should get what you want.



Stéphane Téletchéa, PhD.                  http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
INRA, Domaine de Vilvert                  Tél : (33) 134 652 891
78352 Jouy-en-Josas cedex, France         Fax : (33) 134 652 901

More information about the gromacs.org_gmx-users mailing list