[gmx-users] Creation of an index file with seperate lipid leaflets
Patrick.Fuchs at ebgm.jussieu.fr
Thu Nov 9 14:02:26 CET 2006
I've written a python script that does what you want.
I cleaned the script (make_2leaflets_index) and put it on my web page at
the following URL:
Hope it helps.
Jay Mashl a écrit :
> 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.
> 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
>>>> file with the atoms from the two leaflets of a
>>>> listed seperately? I can't believe it hasn't
>>>> been done, but can't find a direct description of
>>>> solution. I'm attempting a modification to
>>>> (or perhaps something considerably less ambitious,
>>>> judging by the way it's going so far) to permit
>>>> selection based on headgroup orientation, though
>>>> 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
>>> Reordering the lipids into leaflets in your starting
>>> 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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