[gmx-users] Re: individual lateral diffusion coefficients

Javier Cerezo jcb1 at um.es
Thu Dec 2 16:40:13 CET 2010 

Thanks Justin.

Do you 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
>>> -- 
>>> gmx-users mailing list    gmx-users at gromacs.org 
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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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