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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