Xavier, Thanks for the reply. I'm running of analysis now on my original, non-ordered trajectories. I'll report back to the list with what I come up with.
-Justin Quoting Xavier Periole <[EMAIL PROTECTED]>: > On Fri, 11 Jan 2008 14:29:34 -0500 > "Justin A. Lemkul" <[EMAIL PROTECTED]> wrote: > > Hi all, > > > > I have 100-ns trajectories of a membrane protein embedded in a lipid > bilayer > >and > > I am trying to compute the lateral diffusion coefficients of the lipids in > > different "shells" around the protein. Everything was going fine until I > > re-checked the documentation, at which point I got a little confused. Can > > someone please help me sort out what I need to do to get the correct > lateral > > diffusion coefficients of my lipids? > > > > I have an ordered trajectory (from trjorder), with the lipids ordered > >according > > to their distance from the protein. > > The major problem I think you are facing is the fact that you use an > ordered trajectory. Then the lipids are ordered according to their > distance from the protein for each frame. This means that then in g_msd > you are analyzing discontinuous trajectory. g_msd considers that the > lipid number 2 is the same at each frame. In the ordered trajectory > the lipid number 2 might be going from one side to the other of the > protein. > In conclusion: you do not want to use an ordered trajectory to calculate > the msd of the lipids. > On thing you could do is cut the lipid trajectories in pieces depending > how far they are from the protein and then average over all pieces > of trajectories. The "large" unmber of trajectories might compensate > for their short length. Although for lipids you might actually have > simulations of reasonable length, as compare to water molecules. > > XAvier > > > > > When I issue the command: > > > > g_msd -f ../../TrajFiles/ordered.xtc -s ../md.tpr -n ../lipids_shells.ndx > -o > > msd_shells.xvg -ngroup 4 -lateral y -trestart 1000 > > (and subsequently selecting each of my four index groups) > > > > I get output of lateral diffusion coefficients for each group. The index > >group > > specified has the lipids by their molecule number, which brings me to my > >first > > question: Is that the proper index group to use if I am not specifying > -mol? > > Some of my results come up negative, and I see from the archive from DvdS > >that > > this is due to poor single molecule statistics, but I my index file > >specifies > > multiple molecules in a shell. I suspect this is a problem with the index > > file? Do I have to specify the desired group in terms of all the atoms in > >the > > lipids of interest? > > > > When I issue: > > > > g_msd -f ../../TrajFiles/ordered.xtc -s ../md.tpr -n ../lipids_shells.ndx > -o > > msd_shells.xvg -mol msd_mol_shells.xvg -ngroup 4 -lateral y -trestart 1000 > > (please note the use of the same index file) > > > > I get a very different result. The lateral diffusion coefficients in > > msd_shells.xvg are two orders of magnitude larger than in the first result, > >and > > the msd_mol_shells.xvg is filled with mostly 'nan' entries. Is this > because > >of > > some incompatibility between -ngroup and -mol? > > > > I have found in the list archives that the number without the -mol option > is > > more accurate due to statistical sampling, but that seems to contradicts > the > > manual entry for g_msd. Hence my confusion. > > > > Thanks in advance for any comments and hints. > > > > -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 gmx-users@gromacs.org > > 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 > > ----------------------------------------------------- > XAvier Periole - PhD > > NMR & Molecular Dynamics Group > University of Groningen > The Netherlands > http://md.chem.rug.nl/~periole > ----------------------------------------------------- > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users@gromacs.org 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