[gmx-users] Re: individual lateral diffusion coefficients

Thu Dec 2 23:23:09 CET 2010

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
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