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

[Alan Dodd]

Wouldn't shuffle/sort undo all the good work?  I did
wonder if I should have labelled the lipids in
different leaflets as different molecule types, or
different chains, but it's a bit late now...

--- Jay Mashl <mashl at uiuc.edu> wrote:

> 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.
> 
> Jay
> 
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