[gmx-users] Re: individual lateral diffusion coefficients

[Javier Cerezo]

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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