[gmx-users] individual lateral diffusion coefficients

[Justin A. Lemkul]

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¿?
> 

In my experience, this is to be expected.  To calculate reliable diffusion 
coefficients, you need very well-converged data, and for individual lipids, this 
effect is even more pronounced.  How long is your trajectory, and how often did 
you save snapshots?

Note too, that the results of g_msd can be impacted by -trestart, -beginfit, 
-endfit, etc.

-Justin

> Thanks for any advice
> 
> Ángel Piñeiro.
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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