On Sun, Aug 23, 2009 at 7:32 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > > Actually when I open autocorr.xvg I can see from data/feature >> extraction/ the last set is S1295 (N=101, autocorr.xvg) which means >> they are 1296 graphs each with poor statistics start at 1 and coming >> down. To have a ACF for a system I expect to get one graph with good >> statistic... I hope I make it clear now. >> > > What did you extract with g_traj? All the coordinates of all the > molecules? The command line you gave would be helpful here. It would seem > that 1296/216 = 6, therefore (and this is just a guess) then g_analyze is > trying to calculate some sort of ACF between all coordinates: x-x, y-y, z-z, > x-y, x-z, y-z. That way, you'd be getting these ACF's for each individual > molecule. Again, just a guess. Hi Justin, I think that I extract only the coordinates for my desired atoms using this command: g_traj -f f.xtc -s f.tpr -n f.ndx -ox coord.xvg and then g_analyze -f coord.xvg -ac autocorr.xvg Is that the way to get ACF or I am doing something wrong here?? Many Thanks in Advance/Jamie > > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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