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Sorry for the misspell...<br>
<blockquote cite="mid:4CF7BDDD.9090402@um.es" type="cite">Thanks
Justin.
<br>
<br>
Do you <b>know</b> the reason behind?
<br>
<br>
I am trying following that protocol and my P curve in not as linear as
All-lipid-atoms one (DPPC, FF: G53a6, t=50ns). Furthermore, regarding
the linear region, the slopes are not the same. So which one do you
think is more accurate?
<br>
<br>
Thanks again
<br>
<br>
Javier
<br>
<br>
El 02/12/10 16:09, Justin A. Lemkul escribió:
<br>
<blockquote type="cite"><br>
<br>
Ángel Piñeiro wrote:
<br>
<blockquote type="cite">Hi Javier
<br>
I think I saw this in several mails of this list and it is also
implicit in the Justin tutorial for analysis of bilayers. I am not sure
whether or not this has also been published... I do not remember any
paper. I think this is reasonable for lipids in contact with membrane
proteins because only a part of the lipid could be "tied" to the
protein... then the diffusion for different parts of the lipid could be
different.
<br>
<br>
I think I will calculate the diffusion for each lipid individually...
<br>
<br>
If you are interested in comparing results you could contact me off the
list.
<br>
<br>
</blockquote>
<br>
I haven't followed this thread at all, but I saw my name come up :)
This is what I have always based my g_msd calculations on:
<br>
<br>
<a class="moz-txt-link-freetext" href="http://lists.gromacs.org/pipermail/gmx-users/2008-January/031804.html">http://lists.gromacs.org/pipermail/gmx-users/2008-January/031804.html</a>
<br>
<br>
-Justin
<br>
<br>
<blockquote type="cite">Saludos,
<br>
<br>
Ángel.
<br>
<br>
<br>
<br>
<br>
On Thu, 2010-12-02 at 14:22 +0100, Javier Cerezo wrote:
<br>
<blockquote type="cite">Hi Ángel
<br>
<br>
Can you provide a citation about the use of only PO4 atoms to calculate
the diffusion constant? Is it always recommended or just with CG
simulations? I'm also working on diffusion calculation and that will be
interesting.
<br>
<br>
By the way, regarding the index files I mentioned, it might be better
to have a group of lipids that are at a certain distance from the
protein in the same index, again to improve sampling (maybe this is not
a way to improve sampling, I don't know).
<br>
<br>
Thanks
<br>
<br>
Javier
<br>
<br>
<br>
El 02/12/10 13:56, Ángel Piñeiro escribió:
<br>
<blockquote type="cite">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>
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
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</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
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gmx-users mailing list <a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>
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</blockquote>
<br>
</blockquote>
<br>
</blockquote>
<br>
</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
</pre>
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