Hi Ángel
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.
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).
Thanks
Javier
El 02/12/10 13:56, Ángel Piñeiro escribió:
Hi Javier
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
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
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" ;)
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...
Thanks for your reply!
Ángel.
On Thu, 2010-12-02 at 13:30 +0100, Javier Cerezo wrote:
Hello Ángel.
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:
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).
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).
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).
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.
Good luck
Javier
El 02/12/10 12:50, Ángel Piñeiro escribió:
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.
--
Javier CEREZO BASTIDA
Estudiante de Doctorado
---------------------
Dpto. Química-Física
Universidad de Murcia
30100 MURCIA (España)
Tlf.(+34)868887434
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Javier CEREZO BASTIDA
Estudiante de Doctorado
---------------------
Dpto. Química-Física
Universidad de Murcia
30100 MURCIA (España)
Tlf.(+34)868887434
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