[gmx-users] About and index file of a monolayer...

Joe Jordan e.jjordan12 at gmail.com
Mon Feb 26 18:32:00 CET 2018

This is actually pretty challenging to do, but is possible with the right
technique. Have a look at the selection commands in gmx select, which
allows the specification of x,y,z positions. If you know the mid plane of
one leaf in your bilayer, you can specify a molecule type and only take
molecules that have a center of mass within a cutoff of the leaflet mid
plane (which hopefully is on xy plane with fixed z). If you have a large
enough bilayer you may have undulations, which means that you will need to
make a more complicated selection, specifying x, y and z.

On Mon, Feb 26, 2018 at 5:58 PM, Poncho Arvayo Zatarain <
poncho_8629 at hotmail.com> wrote:

> Hello gromacs users: If i have a bilayer with lipids A & B and i want to
> create an index file for the upper and lower monolayer of one lipid, for
> example: lipid A-UPPER and lipid B-UPPER. Also, lipid A-LOWER and lipid
> B-UPPER. How can i do that using -n index.file?
> --
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Joe Jordan

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