Dear Javier, Justin, Xavier... Thank you very much for your feedback. Finally I decided to create a group for each PO4 in my system and calculate all the individual diffusion values. I also plotted all the MSDs as a function of time and took a safe -beginfit -endfit interval for the fittings. I think that I took a very short interval (only 25 ns) but after that time the MSD slope changes for some lipids (in some cases it becomes negative!). I guess I should try with different -trestart values... I saved snapshots every 150 ps. My bilayer trajectories (without protein) are 2 microseconds long (note that I am using Martini) but I decided to do this analysis after the first microsecond.
The command I am using within a loop which runs over all the lipids is something like: g_msd -s topol.tpr -f traj.xtc -n p.ndx -b 1000000 -e 1150000 -trestart 1000 -lateral z -rmcomm -beginfit 1500 -endfit 25000 And the dispersion between individual diffusion values is much lower now... with these parameters they range between 0.04 and 0.25 (x 10-5 cm2 s-1) I will try with different trestart values but it seems that I am closer now... I will follow testing with pure bilayers for a while... My simulations with proteins are 5 microseconds long. I plan to calculate the protein-lipid distance for all the lipids as a function of time over the last 0.5 microsecond or so and then I would have arguments to discuss the corresponding diffusion values. Hope this is reasonable... Greetings, Ángel. On Thu, 2010-12-02 at 19:14 +0100, XAvier Periole wrote: > Dear Angel, > > I agree with Justin comments and I might add: > > Taken from the marrink-2004JPC martini paper: > "Microsecond simulations of the bilayer containing 256 > DPPC molecules allows the observation of truely long > time diffusive behavior. At T = 323 K, the lateral diffusion > rates of DPPC equals 3 +/-1 10-7 cm2 s-1, of the same > order of magnitude as experimentally measured (values > are typically reported to be around 1 10-7 cm2 s-1 at > temperatures close to 323 K; e.g., see refs 38 and 39)" > > Here a factor 4 is used to scale the CG dynamics, your > simulation is fine. I am however surprised by the variance of > your individual lipids ... the length of your simulation might > be the reason ... > > We have looked at lipid/protein interaction with Martini > quite a lot and convergence is reached after a few > microseconds and a multitude of exchanges of lipids > between contacts with the protein and the bulk. You'd > then have the issue of which lipid to consider in which > section ... not a trivial choice. > > XAvier. > > On Dec 2, 2010, at 12:50 PM, Ángel Piñeiro wrote: > > > 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. > >> > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search > > before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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