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Hello Ángel.<br>
<br>
Well, there are a some things that I don't understand about your
calculation, but might be just a problem of mine. Here you have my
comments:<br>
<br>
1. How do you get the diff_mol.xvg file if you are not using -mol in
your command line input (and you index file has broken molecules).<br>
<br>
2. Why do you select just an atom to calculate the diffusion? According
to Wolhert and Edholm (JCP, 125, 204703) the MSD for all lipids atoms
reach the same slope, so I guess using them all could improve sampling
(I'm not sure).<br>
<br>
3. I think that reprocessing of your trajectory to remove jumps is no
longer needed (I got the same results in a recent test using version
4.5.1).<br>
<br>
4. What I would do to calculate D as funtion to the distance to the
membrane protein is generate different index files containing lipids
according to this distance (and hoping they don't move a lot during the
simulation) and run different msd calculations. I think I have read in
the mailing list about a script to make such a selection regarding
distances to construct the index file or just make your own one.<br>
<br>
Good luck<br>
<br>
Javier <br>
<br>
El 02/12/10 12:50, Ángel Piñeiro escribió:
<blockquote cite="mid:1291290610.25260.2755.camel@arginine" type="cite">
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I want to add that the MSD as a function of time (msd.xvg file) looks
completely linear<br>
<br>
Greetings,<br>
<br>
Ángel Piñeiro.<br>
<br>
On Thu, 2010-12-02 at 12:45 +0100, Ángel Piñeiro wrote:<br>
<blockquote type="CITE"> Dear all,<br>
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:<br>
<br>
g_msd -s topol.tpr -f trajnojump.xtc -n p.ndx -lateral z -rmcomm<br>
<br>
from which I get the following output:<br>
D[ PO4] 0.0958 (+/- 0.0135) 1e-5 cm^2/s<br>
<br>
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¿?<br>
<br>
Thanks for any advice<br>
<br>
Ángel Piñeiro.<br>
<br>
</blockquote>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Javier CEREZO BASTIDA
Estudiante de Doctorado
---------------------
Dpto. Química-Física
Universidad de Murcia
30100 MURCIA (España)
Tlf.(+34)868887434
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