[gmx-users] About gmx msd and membrane leaflets

[Alessandra Villa]

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.

Best regards
Alessandra



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