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Javier<BR>
is your system a pure lipid bilayer + solvent or is there anything else (protein, peptides, etc)?<BR>
<BR>
Cheers <BR>
<BR>
Ángel.<BR>
<BR>
<BR>
On Fri, 2010-12-03 at 00:42 +0100, Javier Cerezo wrote:
<BLOCKQUOTE TYPE=CITE>
<PRE>
Hi.
I think that these arguments are given for short-time diffusion (D1).
But at larger times all MSD curves reach the same slope, so all of them
have the same brownian diffusion (D2).
Then, I wonder if taking all the atoms, which means more points to
average, will results in better statistics and thus better results (even
for not such a long times). Does it make sense or am I overseeing
fundamental physical meaning?
Thanks
Javier
Dallas Warren escribió:
>
> It seems to me that it will be for the reasons mentioned in the paper
> <A HREF="http://dx.doi.org/10.1063/1.2393240">http://dx.doi.org/10.1063/1.2393240</A> <<A HREF="http://dx.doi.org/10.1063/1.2393240">http://dx.doi.org/10.1063/1.2393240</A>>
>
>
>
> By focusing on the phosphate atom, you are measuring the actual
> movement of the entire lipid molecule within the membrane, which is
> the diffusion that is measured typically experimentally. If you use
> the entire molecule, then you get the movement of the alkane chains as
> well, which increase the diffusion coefficient by more than a factor
> of ten.
>
>
>
> Catch ya,
>
> Dr. Dallas Warren
>
> Medicinal Chemistry and Drug Action
>
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> <A HREF="mailto:dallas.warren@monash.edu">dallas.warren@monash.edu</A>
>
> +61 3 9903 9304
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to
> resemble a nail.
>
>
>
> *From:* <A HREF="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</A>
> [<A HREF="mailto:gmx-users-bounces@gromacs.org">mailto:gmx-users-bounces@gromacs.org</A>] *On Behalf Of *Javier Cerezo
> *Sent:* Friday, 3 December 2010 2:46 AM
> *To:* <A HREF="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A>
> *Subject:* Re: [gmx-users] Re: individual lateral diffusion coefficients
>
>
>
> Sorry for the misspell...
>
> Thanks Justin.
>
> Do you *know* 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:
>
> <A HREF="http://lists.gromacs.org/pipermail/gmx-users/2008-January/031804.html">http://lists.gromacs.org/pipermail/gmx-users/2008-January/031804.html</A>
>
> -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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>
>
>
> --
> Javier CEREZO BASTIDA
> Estudiante de Doctorado
> ---------------------
> Dpto. Química-Física
> Universidad de Murcia
> 30100 MURCIA (España)
> Tlf.(+34)868887434
--
Javier CEREZO BASTIDA
Estudiante de Doctorado
---------------------
Dpto. Química-Física
Universidad de Murcia
30100 MURCIA (España)
Tlf.(+34)868887434
</PRE>
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