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Hi Javier<BR>
1.- you are right! the diff_mol.xvg file I reported was from a previous attempt in which I used the whole lipid molecules with the -mol option on, instead of the PO4 beads with -mol off. Sorry for this confusion<BR>
<BR>
2.- As I said above, I did attempts using both the whole molecule and the PO4 beads. Yes I saw the figure 6 in the Wolhert &Edholm's paper but I read in several other references that the calculation is more accurate by using only the P atom... what makes sense to me mainly for the lipids which are in contact with proteins<BR>
<BR>
3.- I agree that removing jumps does not change anything. I decided to give this information in my message to avoid a reply saying "try to remove jumps" ;)<BR>
<BR>
4.- Yes I agree that I could do the calculation by creating an index for each lipid... I guess that is the safest way to proceed... <BR>
<BR>
Thanks for your reply!<BR>
<BR>
Ángel.<BR>
<BR>
<BR>
<BR>
On Thu, 2010-12-02 at 13:30 +0100, Javier Cerezo wrote:<BR>
<BLOCKQUOTE TYPE=CITE>
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: <BR>
<BLOCKQUOTE TYPE=CITE>
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>
-- <BR>
Javier CEREZO BASTIDA<BR>
Estudiante de Doctorado<BR>
---------------------<BR>
Dpto. Química-Física<BR>
Universidad de Murcia<BR>
30100 MURCIA (España)<BR>
Tlf.(+34)868887434<BR>
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