Hi Giordano, Do you have a conformational change? If you consider unidirectional motion, in one or N coordinates alike, you would expect just what you see for the fluctuations. In fact, it's not really fluctuation then. 10 ns is also pretty short for a simulation of a protein. It's likely that you're analyzing relaxation from the starting structure.
Cheers, Tsjerk On Tue, Oct 7, 2008 at 8:03 PM, giordano mancini <[EMAIL PROTECTED]> wrote: > Hi all, > > I have the following problem: I have a simulation > of 10 ns of a protein in water. I have extracted the protein trajectory > with trjconv -pbc nojump and the fitted it to a reference structure > with trjconv -fit rot+trans. > If I run g_rmsf -nofit over two consecutive chunks of 5 ns i get very > similar rmsf values (so the fluctuations are are the same in the 2 time > windows). However if I run g_rmsf over the whole trajectory i get much > higher values of rmsf (up to 0.1 - 0.15 nm). The difference become higher if > use 4 windows of 2.5 ns each (i.e. the rmsf over 2.5 ns are smaller). > I think there's something wrong with the reference structure which is > different in the various cases so that with shorter trajectories the std > dev is smaller; however I always use the same .gro (or tpr). May be are > the -b and -e flags? > Use of tpr/gro reference, fit with g_rmsf, calpha or backbone, > or -res option does not change things. > I have tried with gromacs 3.3.1 and 3.3.3 > > Here 's my complete syntax: > > $> trjconv -s box.gro -f nojump.xtc -n index.ndx -o nj -pbc nojump > $> trjconv -s box.gro -f nj.xtc -n index -fit rot+trans -o fitted > $> g_rmsf -s box.gro -f fitted -n index -o rmsf$start -b $start -e $end > for chuncks > > $> g_rmsf -s box.gro -f fitted -n index -o rmsf > > thanks for your help > giordnao mancini > > _______________________________________________ > 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 > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ 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
