Thanks Justin!
On 10/17/11, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Tom wrote: >> Justin >> >> you have good experience of pulling. >> >> If you have time, please help with this publling problem: >> abrupt change in sign of 1dZ on output file: pullx.xvg. Thanks a lot! >> > > I already commented: > > http://lists.gromacs.org/pipermail/gmx-users/2011-October/065226.html > >> i am pulling A object towards B along z-axis. But system >> has pbc on x, y and z. Is it because of the pbc image of B >> object that make grmx confused to report the sign. >> > > Likely. If your box is not greater than about 16.3 nm in Z, then you'll > have > this problem. > >> In my system, A should be on the top of B in z-axis, but i just noticed >> that at the intial step: 1dZ has been negative already. >> It seems the system use the PBC image (in z-axis) of the reference object >> B >> to cacluate 1dZ, right? > > Sounds right. > > -Justin > >> -------------------------------------- >> @ title "Pull COM" >> @ xaxis label "Time (ps)" >> @ yaxis label "Position (nm)" >> @TYPE xy >> @ view 0.15, 0.15, 0.75, 0.85 >> @ legend on >> @ legend box on >> @ legend loctype view >> @ legend 0.78, 0.8 >> @ legend length 2 >> @ s0 legend "0 Z" >> @ s1 legend "1 dZ" >> 0.0000 0.77622 -8.13474 >> ------------------------------------ >> >> Thanks a lot for the help! >> >> Tom >> >> ---------- Forwarded message ---------- >> From: Tom <dna...@gmail.com> >> Date: Sun, 16 Oct 2011 23:02:09 +0800 >> Subject: about the pulling >> To: gmx-users <gmx-users@gromacs.org> >> >> Dear Gromacs Users or Developers, >> >> I am using the pulling the COM of object A towards B using: >> --------------------------------- >> pull = umbrella >> pull_geometry = distance >> pull_dim = N N Y >> pull_start = yes >> pull_ngroups = 1 >> pull_group0 = B >> pull_group1 = A >> pull_rate1 = -0.00005714 >> pull_k1 = 5000 >> ------------------------------- >> On the output file of pullx.xvg, the sign of dZ >> has been changed from negative to posivitve >> or vice vrsa in all sudden. What does it mean? >> >> The following is an example: >> >> @ title "Pull COM" >> @ xaxis label "Time (ps)" >> @ yaxis label "Position (nm)" >> @TYPE xy >> @ view 0.15, 0.15, 0.75, 0.85 >> @ legend on >> @ legend box on >> @ legend loctype view >> @ legend 0.78, 0.8 >> @ legend length 2 >> @ s0 legend "0 Z" >> @ s1 legend "1 dZ" >> >> --------------------------------------------------- >> 173.7400 0.77622 8.14856 >> 173.7500 0.77622 8.14897 >> 173.7600 0.77622 8.14938 >> 173.7700 0.77622 8.14977 >> 173.7800 0.77622 -8.14987 >> 173.7900 0.77622 -8.14954 >> 173.8000 0.77622 -8.14924 >> 173.8100 0.77622 -8.14895 >> ------------------------------------ >> >> >> Thanks a lot for the information! >> >> Thanks, >> >> Tom >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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/Support/Mailing_Lists/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/Support/Mailing_Lists