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

[Jay Mashl]

Wasted work would be bad ;)

Rather than headgroup orientation, maybe try looking at atom distributions 
along the bilayer normal direction.  Neutron scattering experiments show that 
for atom groups far from the bilayer midplane, the corresponding z-coordinates 
form two distinct distributions.  So one way could be the following. Pick a 
headgroup atom and obtain its z-coordinate. Have make_ndx accept this value as 
input. Search the system by looping over lipids and ask whether that atom type 
has a z-coordinate within some amount around the input value. From this you 
know the membership of the leaflets.  A more automatic way would be to have the 
program first discern the distribution and then reread the system to decide the 
leaflet membership.

Jay


On Wed, 8 Nov 2006, Alan Dodd wrote:
> 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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> 
> 
> 
>  
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-- 
R. Jay Mashl
University of Illinois
mashl at uiuc.edu
(Tel)217-244-5818