[gmx-users] Re: individual lateral diffusion coefficients

[Ángel Piñeiro]

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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