[gmx-users] Re: individual lateral diffusion coefficients

[Ángel Piñeiro]

Dear Javier, Justin, Xavier...
Thank you very much for your feedback. Finally I decided to create a
group for each PO4 in my system and calculate all the individual
diffusion values. I also plotted all the MSDs as a function of time and
took a safe -beginfit -endfit interval for the fittings. I think that I
took a very short interval (only 25 ns) but after that time the MSD
slope changes for some lipids (in some cases it becomes negative!). I
guess I should try with different -trestart values... I saved snapshots
every 150 ps. My bilayer trajectories (without protein) are 2
microseconds long (note that I am using Martini) but I decided to do
this analysis after the first microsecond. 

The command I am using within a loop which runs over all the lipids is
something like:

g_msd -s topol.tpr -f traj.xtc -n p.ndx -b 1000000 -e 1150000 -trestart
1000 -lateral z -rmcomm -beginfit 1500 -endfit 25000

And the dispersion between individual diffusion values is much lower
now... with these parameters they range between 0.04 and 0.25 (x 10-5
cm2 s-1)

I will try with different trestart values but it seems that I am closer
now... I will follow testing with pure bilayers for a while... My
simulations with proteins are 5 microseconds long. I plan to calculate
the protein-lipid distance for all the lipids as a function of time over
the last 0.5 microsecond or so and then I would have arguments to
discuss the corresponding diffusion values. Hope this is reasonable...

Greetings,

Ángel.


On Thu, 2010-12-02 at 19:14 +0100, XAvier Periole wrote:

> 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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