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
