[gmx-users] CG lipid diffusion coefficient

[Peter Kroon]

Dear Yasser,


A factor of 100 is kind of a lot indeed, and should prompt further
investigation.

What phase (gel, liquid disordered, ...) is your bilayer in? Is it
homogeneous? Is it the same as the phase for your reference value?

The 2009 paper probably uses a different mapping scheme/topology for
some lipids, which will affect the diffusion behaviour. Could you run
some pure bilayers to double check some of the values?

How are the static bilayer properties (apl, thickness, ...)?


Peter



On 29-03-19 13:48, Yasser Almeida Hernández wrote:
> Hi all,
>
> I ran some CG simulations of a protein inserted in a lipid bilayer,
> with several lipids. I used the msd tool to compute the lipid (using
> the PO4) diffusion coefficient. For one of the lipid I got D = 0.6 x
> 10^-5 cm^2/s, which is 600 um^2/s. According to the Martini website
> "To compare the diffusion coefficient obtained from a Martini
> simulation to a measured one, a conversion factor of about 4 has to be
> applied to account for the faster diffusion at the CG level due to the
> smoothened free energy landscape (note, the conversion factor can vary
> significantly depending on the molecule in question)." (J Phys Chem B.
> 2009 Feb 5; 113(5): 1501–1510.)
>
> The value I get is 2 orders of magnitude higher of a comparable value
> of 6 um^2/s.
>
> Would this make sense?
>
> Regards
>
> Yasser
>