[gmx-users] Re: individual lateral diffusion coefficients

[XAvier Periole]

Dear Angel,

I agree with Justin comments and I might add:

Taken from the marrink-2004JPC martini paper:
"Microsecond simulations of the bilayer containing 256
DPPC molecules allows the observation of truely long
time diffusive behavior. At T = 323 K, the lateral diffusion
rates of DPPC equals 3 +/-1 10-7 cm2 s-1, of the same
order of magnitude as experimentally measured (values
are typically reported to be around 1 10-7 cm2 s-1 at
temperatures close to 323 K; e.g., see refs 38 and 39)"

Here a factor 4 is used to scale the CG dynamics, your
simulation is fine. I am however surprised by the variance of
your individual lipids ... the length of your simulation might
be the reason ...

We have looked at lipid/protein interaction with Martini
quite a lot and convergence is reached after a few
microseconds and a multitude of exchanges of lipids
between contacts with the protein and the bulk. You'd
then have the issue of which lipid to consider in which
section ... not a trivial choice.

XAvier.

On Dec 2, 2010, at 12:50 PM, Ángel Piñeiro wrote:

> 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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