[gmx-users] Re: individual lateral diffusion coefficients

Thu Dec 2 15:38:30 CET 2010

Hi Javier
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.

I think I will calculate the diffusion for each lipid individually... 

If you are interested in comparing results you could contact me off the
list.

Saludos,

Ángel.

On Thu, 2010-12-02 at 14:22 +0100, Javier Cerezo wrote:

> 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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