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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