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

[Oliver Beckstein]

> On Feb 26, 2018, at 10:31 AM, Joe Jordan <e.jjordan12 at gmail.com> wrote:
> 
> 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.

If the membrane is flat then the above approach should work.

For more complicated shapes of the membrane you could try the LeafletFinder algorithm (implemented in MDAnalysis https://www.mdanalysis.org/docs/documentation_pages/analysis/leaflet.html <https://www.mdanalysis.org/docs/documentation_pages/analysis/leaflet.html> , see reference there or go directly to https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3144279/#S9 <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3144279/#S9> ). It’s not very complicated so you could write your own code (and perhaps contribute it to Gromacs) or try out the code in MDAnalysis and write out a Gromacs index file. 

(Please note: if you have any questions about MDAnalysis then ask on https://groups.google.com/forum/#!forum/mdnalysis-discussion <https://groups.google.com/forum/#!forum/mdnalysis-discussion> and NOT on the Gromacs mailing list.)

I don’t think that Gromacs tools have this functionality at the moment so that’s why I am pointing to external tools.

Disclosure: I am one of the MDAnalysis developers.

> 
> 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?
>> --
>> Gromacs Users mailing list
>> 
>> * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/GMX-Users_List before posting!
>> 
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> 
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>> 
> 
> 
> 
> -- 
> Joe Jordan
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

Best wishes,
Oliver Beckstein

--
Oliver Beckstein, DPhil * oliver.beckstein at asu.edu
http://becksteinlab.physics.asu.edu/

Assistant Professor of Physics
Arizona State University
Center for Biological Physics and Department of Physics
Tempe, AZ 85287-1504
USA
	
Office: PSF 348
Phone: +1 (480) 727-9765
FAX: +1 (480) 965-4669

Department of Physics: https://physics.asu.edu/content/oliver-beckstein
Center for Biological Physics: https://cbp.asu.edu/content/oliver-beckstein