On 3/18/20 4:50 AM, Alessandra Villa wrote:
Hi,
On Tue, Mar 17, 2020 at 11:15 PM Poncho Arvayo Zatarain <
poncho_8...@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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