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@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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