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 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. 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? -------------------------------------- @ 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 -- 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
