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
