[gmx-users] Re: individual lateral diffusion coefficients

Ángel Piñeiro angel.pineiro at usc.es
Fri Dec 3 09:52:32 CET 2010 

Javier
is your system a pure lipid bilayer + solvent or is there anything else
(protein, peptides, etc)?

Cheers 

Ángel.


On Fri, 2010-12-03 at 00:42 +0100, Javier Cerezo wrote:

> Hi.
> 
> I think that these arguments are given for short-time diffusion (D1). 
> But at larger times all MSD curves reach the same slope, so all of them 
> have the same brownian diffusion (D2).
> 
> Then, I wonder if taking all the atoms, which means more points to 
> average, will results in better statistics and thus better results (even 
> for not such a long times). Does it make sense or am I overseeing 
> fundamental physical meaning?
> 
> Thanks
> 
> Javier
> 
> Dallas Warren escribió:
> >
> > It seems to me that it will be for the reasons mentioned in the paper 
> > http://dx.doi.org/10.1063/1.2393240 <http://dx.doi.org/10.1063/1.2393240>
> >
> >  
> >
> > By focusing on the phosphate atom, you are measuring the actual 
> > movement of the entire lipid molecule within the membrane, which is 
> > the diffusion that is measured typically experimentally.  If you use 
> > the entire molecule, then you get the movement of the alkane chains as 
> > well, which increase the diffusion coefficient by more than a factor 
> > of ten.
> >
> >  
> >
> > Catch ya,
> >
> > Dr. Dallas Warren
> >
> > Medicinal Chemistry and Drug Action
> >
> > Monash Institute of Pharmaceutical Sciences, Monash University
> > 381 Royal Parade, Parkville VIC 3010
> > dallas.warren at monash.edu
> >
> > +61 3 9903 9304
> > ---------------------------------
> > When the only tool you own is a hammer, every problem begins to 
> > resemble a nail.
> >
> >  
> >
> > *From:* gmx-users-bounces at gromacs.org 
> > [mailto:gmx-users-bounces at gromacs.org] *On Behalf Of *Javier Cerezo
> > *Sent:* Friday, 3 December 2010 2:46 AM
> > *To:* gmx-users at gromacs.org
> > *Subject:* Re: [gmx-users] Re: individual lateral diffusion coefficients
> >
> >  
> >
> > Sorry for the misspell...
> >
> > Thanks Justin.
> >
> > Do you *know* the reason behind?
> >
> > 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?
> >
> > Thanks again
> >
> > Javier
> >
> > El 02/12/10 16:09, Justin A. Lemkul escribió:
> >
> >
> >
> > Ángel Piñeiro wrote:
> >
> > 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.
> >
> >
> > 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:
> >
> > http://lists.gromacs.org/pipermail/gmx-users/2008-January/031804.html
> >
> > -Justin
> >
> >
> > 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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> >  
> >
> >  
> >
> >  
> >
> >
> >
> > -- 
> > Javier CEREZO BASTIDA
> > Estudiante de Doctorado
> > ---------------------
> > Dpto. Química-Física
> > Universidad de Murcia
> > 30100 MURCIA (España)
> > Tlf.(+34)868887434
> 
> -- 
> Javier CEREZO BASTIDA
> Estudiante de Doctorado
> ---------------------
> Dpto. Química-Física
> Universidad de Murcia
> 30100 MURCIA (España)
> Tlf.(+34)868887434
> 
> 
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