[gmx-users] Re: individual lateral diffusion coefficients

[Ángel Piñeiro]

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.
> 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101202/d4bd0dc7/attachment.html>