Patrick, Thanks for pointing this paper out. I'll have a look at it. As for now, I'm following David's advice and will see where that takes me.
-Justin Quoting Patrick Fuchs <[EMAIL PROTECTED]>: > Hi Justin, > Wohlert and Edholm (http://dx.doi.org/10.1063/1.2393240) suggested to > extract the motion of the 2 monolayers relative to each other, before > calculating the MSD. This is an artefact coming from the finite size of > computer simulations. This may explain the discrepancy you get between > both leaflets. > Second, they showed that there are two different diffusions. A fast > diffusion occuring on ps time scale and a longer one which is brownian > and can be compared to FRAP experiments. In their paper, they propose a > fitting procedure that extracts both diffusion constants. Furthermore, > be sure to equilibrate enough (a few tens of ns) before doing this analysis. > Cheers, > > Patrick > > Justin A. Lemkul a écrit : > > Hi Alan, > > > > Thanks for the reply. My initial trajectory showed several of the lipids > jumped > > across the box and continued through the bilayer from there, which resulted > in a > > large displacement, so I processed the trajectory with trjconv -pbc nojump. > > There is still a rather large initial displacement (within the first > several > > nanoseconds out of 100, likely due to my equilibration procedure of packing > the > > lipids tightly around the peptide), so I attempted to analyze the last 75 > ns and > > 90 ns of the trajectory, using the structures at those times as the > reference > > (in g_msd -s). Still the same result, a large value of D. > > > > Any ideas? > > > > Thanks again. > > > > -Justin > > > > > > Quoting Alan Dodd <[EMAIL PROTECTED]>: > > > >> What happens if you visualise the trajectory? Two orders of magnitude in > >> scale of lipid movement should stick out like a sore thumb. > >> > >> ----- Original Message ---- > >> From: Justin A. Lemkul <[EMAIL PROTECTED]> > >> To: [email protected] > >> Sent: Wednesday, January 16, 2008 12:27:45 AM > >> Subject: [gmx-users] About g_msd > >> > >> Hello again, > >> > >> I'm back with a few more questions about g_msd (version 3.3, in case I > hadn't > >> mentioned that before). Thanks to Xavier's message earlier, I have > abandoned > >> use of ordered trajectories to analyze my lipids. I will deal with lipid > >> "shells" in the future. For now I am approaching the problem of lateral > >> diffusion coefficients from a slightly different angle. > >> > >> My system contains a helical peptide that is oriented asymmetrically with > >> respect to the DPPC bilayer. It is tilted and only partially embedded > into > >> the > >> intracellular leaflet of the bilayer (at the beginning of the simulation). > >> Due > >> to the asymmetry, I would like to study the properties of the leaflets > >> separately, including, among other parameters, the lateral diffusion > >> coefficients of the component lipids. > >> > >> I have found a few papers that have simulated pure DPPC bilayers, and am > >> using > >> them as somewhat of a reference point for the magnitude of the lateral > >> diffusion coefficients that I am determining: E. Lindahl and O. Edholm > >> (2001) > >> J. Chem. Phys. 115 (10), and U. Essmann and M. L. Berkowitz (1999) > Biophys. > >> J. > >> 76. > >> > >> For the top leaflet of my bilayer, I am getting a value of D = > >> (4.0+/-2.2)x10^-7 > >> cm^2/sec (reasonable, in terms of order of magnitude, I think), but for > the > >> bottom leaflet, I am getting roughly (355.7+/-551.5)x10^-7 cm^2/sec. I > >> figured > >> this enormous number was due to artefacts of PBC, so I tried every > iteration > >> of > >> trjconv -pbc, but to no avail. Every result is quite similar. I tried > >> starting g_msd at a later time (10 ns, 25 ns) to determine if any large > >> initial > >> movements of lipids were responsible for the result, but I'm still coming > up > >> with the enormous value of D (albeit slightly lower, ~200+/-400) > >> > >> I am using g_msd -mol, with an index file that contains molecule numbers, > and > >> then using g_analyze on the output .xvg file to get the values of D. > >> > >> Has anyone ever experienced anything similar? Am I missing something > >> obvious? > >> > >> Thanks in advance, as always, especially if you read the entirety of my > >> lengthy > >> message. > >> > >> -Justin > >> > >> > >> ======================================== > >> > >> Justin A. Lemkul > >> Graduate Research Assistant > >> Department of Biochemistry > >> Virginia Tech > >> Blacksburg, VA > >> [EMAIL PROTECTED] | (540) 231-9080 > >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > >> > >> ======================================== > >> _______________________________________________ > >> gmx-users mailing list [email protected] > >> http://www.gromacs.org/mailman/listinfo/gmx-users > >> Please search the archive at http://www.gromacs.org/search before posting! > >> Please don't post (un)subscribe requests to the list. Use the > >> www interface or send it to [EMAIL PROTECTED] > >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >> > >> > >> > >> > > > ____________________________________________________________________________________ > >> Never miss a thing. Make Yahoo your home page. > >> http://www.yahoo.com/r/hs > >> _______________________________________________ > >> gmx-users mailing list [email protected] > >> http://www.gromacs.org/mailman/listinfo/gmx-users > >> Please search the archive at http://www.gromacs.org/search before posting! > >> Please don't post (un)subscribe requests to the list. Use the > >> www interface or send it to [EMAIL PROTECTED] > >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >> > > > > > > > > ======================================== > > > > Justin A. Lemkul > > Graduate Research Assistant > > Department of Biochemistry > > Virginia Tech > > Blacksburg, VA > > [EMAIL PROTECTED] | (540) 231-9080 > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > > > > ======================================== > > _______________________________________________ > > gmx-users mailing list [email protected] > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > -- > _______________________________________________________ > Patrick FUCHS > Equipe de Bioinformatique Genomique et Moleculaire > INSERM U726, Universite Paris 7 > Case Courrier 7113 > 2, place Jussieu, 75251 Paris Cedex 05, FRANCE > Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30 > E-mail : [EMAIL PROTECTED] > Web Site: http://www.ebgm.jussieu.fr/~fuchs > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
