I've been playing with g_msd myself recently, and been seeing weird results toward the end of the simulation. From the below post, it looks like I was doing it correctly (apart from analysing the leaflets separately). Previous posts in the mailing list have implied that increased noise towards the end of a simulation is inherent in the algorithm, I just wanted to check that I was interpreting those posts correctly? And if this is so, do people just not show the results towards the end?
----- Original Message ---- From: David van der Spoel <[EMAIL PROTECTED]> To: Discussion list for GROMACS users <[email protected]> Sent: Wednesday, January 16, 2008 6:48:32 AM Subject: Re: [gmx-users] About g_msd Justin A. Lemkul wrote: > 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? please go back to your original trajectory and do normal g_msd for the P atoms only. (no mol flags etc.) > > 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 -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. 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