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Dear Javier, Justin, Xavier...<BR>
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. <BR>
<BR>
The command I am using within a loop which runs over all the lipids is something like:<BR>
<BR>
g_msd -s topol.tpr -f traj.xtc -n p.ndx -b 1000000 -e 1150000 -trestart 1000 -lateral z -rmcomm -beginfit 1500 -endfit 25000<BR>
<BR>
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)<BR>
<BR>
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...<BR>
<BR>
Greetings,<BR>
<BR>
Ángel.<BR>
<BR>
<BR>
On Thu, 2010-12-02 at 19:14 +0100, XAvier Periole wrote:
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<PRE>
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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