I want to add that the MSD as a function of time (msd.xvg file) looks completely linear
Greetings, Ángel Piñeiro. On Thu, 2010-12-02 at 12:45 +0100, Ángel Piñeiro wrote: > 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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