[gmx-users] Re: individual lateral diffusion coefficients

Thu Dec 2 16:09:25 CET 2010

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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> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================