Javier is your system a pure lipid bilayer + solvent or is there anything else (protein, peptides, etc)?
Cheers Ángel. On Fri, 2010-12-03 at 00:42 +0100, Javier Cerezo wrote: > 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 > > http://dx.doi.org/10.1063/1.2393240 <http://dx.doi.org/10.1063/1.2393240> > > > > > > > > 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 > > dallas.war...@monash.edu > > > > +61 3 9903 9304 > > --------------------------------- > > When the only tool you own is a hammer, every problem begins to > > resemble a nail. > > > > > > > > *From:* gmx-users-boun...@gromacs.org > > [mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Javier Cerezo > > *Sent:* Friday, 3 December 2010 2:46 AM > > *To:* gmx-users@gromacs.org > > *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: > > > > http://lists.gromacs.org/pipermail/gmx-users/2008-January/031804.html > > > > -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 > > -- > > gmx-users mailing list gmx-users@gromacs.org > > <mailto:gmx-users@gromacs.org> <mailto: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 > > <mailto:gmx-users-requ...@gromacs.org> > > <mailto:gmx-users-requ...@gromacs.org>. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > -- > > 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 > > <mailto:gmx-users@gromacs.org> <mailto: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 > > <mailto:gmx-users-requ...@gromacs.org> > > <mailto:gmx-users-requ...@gromacs.org>. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > > > > > > > > > > > -- > > 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 > >
-- 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
