[gmx-users] Re: individual lateral diffusion coefficients

Thu Dec 2 14:22:07 CET 2010

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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