[gmx-users] About gmx msd and membrane leaflets

[Justin Lemkul]

On 3/18/20 4:50 AM, Alessandra Villa wrote:
> Hi,
>
> On Tue, Mar 17, 2020 at 11:15 PM Poncho Arvayo Zatarain <
> poncho_8629 at hotmail.com> wrote:
>
>>
>> Hello gromacs users: I want to obtain the lateral diffusion for a membrane
>> with approximately 55 lipids+ions (NA+Cl) but i want to this for each
>> leaflet of the membrane (outter and inner) and then obtain the average. I
>> know that i can use gmx msd for lateral diffusion, but i don know how to
>> know wich lipids are in each leaftlet. ¿How can separate the leaflets to
>> know wich lipid are in each one? After ¿Can i make an index for each P
>> molecule in each lipid for example and then use it in the gmx msd?
>>
>> yes you can use index file with gmx msd. gmx make_ndx (
> http://manual.gromacs.org/current/onlinehelp/gmx-make_ndx.html) or gmx
> select (http://manual.gromacs.org/current/onlinehelp/gmx-select.html
> <http://manual.gromacs.org/current/onlinehelp/gmx-select.html?highlight=gmx%20select>)may
> help to generate the desired index file.

gmx select is the only way to go here since gmx make_ndx has no ability 
to separate selections based on geometry.

One needs a quick estimate of the middle of the bilayer either from 
coordinates of terminal methyl carbons or using gmx traj. Any P atom 
with z-coordinate less than that value is the lower leaflet; larger 
z-coordinate is the upper leaflet. gmx select can make those selections.

-Justin

> Best regards
> Alessandra
>
>
>
>> Thanks
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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