[gmx-users] Re: individual lateral diffusion coefficients

Justin A. Lemkul jalemkul at vt.edu
Thu Dec 2 19:07:31 CET 2010 


Javier Cerezo wrote:
> 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?
> 

I don't know.  50 ns is somewhat short, I think.  You might have better luck 
with longer trajectories (>100 ns).  In principle (and in a perfect world), all 
force fields would agree, but in reality, this is not the case.  Some models may 
simply perform better than others.

-Justin

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

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