[gmx-users] individual lateral diffusion coefficients

[Ángel Piñeiro]

Dear all,
I aim to calculate the lateral diffusion coefficients of lipids as a
function of the distance to a membrane protein using the Martini force
field. For this I guess I could use the diff_mol.xvg output file of the
g_msd command which provides the list of diffusion coefficients for each
lipid (I guess the lipids are ordered as in the trajectory file). Then I
would calculate the protein-lipid distance for each lipid and I would
generate the diffusion vs distance file. Before starting the
calculations on the membrane protein system I tested the g_msd command
on a DPPC bilayer. In my bilayer simulation I removed the COM of lipids
and water separately. Before analyzing it I removed jumps over the box
boundaries using trjconv -pbc nojump and I created a index file with the
PO4 atoms as a new group. Then I executed the following command:

g_msd -s topol.tpr -f trajnojump.xtc -n p.ndx -lateral z -rmcomm

from which I get the following output:
D[       PO4] 0.0958 (+/- 0.0135) 1e-5 cm^2/s

I think the value is not crazy for DPPC at 323 K using Martini... but I
noticed that the D values for the independent lipids reported in the
diff_mol.xvg file range from 0.0021959 to 0.482909 cm^2/s. If the
differences are so high for a single lipid bilayer I suspect that I will
not observe significant differences as a function of the distance to the
protein in my simulations of the whole system... probably I am doing
something wrong¿?

Thanks for any advice

Ángel Piñeiro.

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