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

Jay Mashl mashl at uiuc.edu
Wed Nov 8 17:09:28 CET 2006

On Wed, 8 Nov 2006, Alan Dodd wrote:
> 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.

Reordering the lipids into leaflets in your starting coordinate 
file might be a good idea. If you anticipate lipid exchange between leaflets, 
then a more general tool like what you suggest would be helpful.


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