Dear Tsjerk, Thanks for your help.
I run the two jobs on a cluster, maybe on different nodes; After just a few hundreds ps, the coordinates of the system differs a lot. When I calculate the distance between two atoms, there is about 1.5A difference; Everything else in mdp file is exactly same. Yours Tanping --- Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote: > Hi Tanping Li, > > Can you be more elaborate? What are the differences? > What do you mean with > "totally different"? Did you run it on the same > machine? Was everything else > the same? > > Cheers, > > Tsjerk > > On 10/5/07, Tanping Li <[EMAIL PROTECTED]> wrote: > > > > Dear all, > > > > I run a 1ns trajectory for a protein in water. by > > accidence, I find that the minor different in mdp > file > > gives two totally different trajectories. By > setting > > > > nstxou=500 > > nstvou=500; > > > > and > > > > nstxou=2500 > > nstvou=2500; > > > > There is very large difference between two > > trajectories (dt=2fs in both cases). I am really > > confused: nstxou JUST sets the frequency to output > the > > coordinate, why I get different results? Looking > > forward to your opinion and thanks a lot. > > > > Yours > > Tanping Li > > _______________________________________________ > > 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 > > > > > > -- > 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 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 _______________________________________________ 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
