Hello everyone, Eventually I want to pull a carbon nanotube through water at a constant rate. Before I get to this, I'm pulling a nanotube in vacuum just to make sure I'm using the pull code correctly.
My system consists of a carbon nanotube aligned along the z axis and a single dummy atom fixed on the z axis. Here is my pull.ppa file: runtype = afm ngroups = 1 group_1 = nanotube pulldim = Y N N reference_group = dummy reftype = com afm_rate1 = 0.1 afm_dir1 = 1 0 0 afm_k1 = 100000 afm_init1 = 2.00 2.00 4.042 Here, the coordinates for afm_init1 is the initial center of mass of the nanotube (thus, the system should start out with zero applied force). Applying this pulling force results in the nanotube undergoing a complicated oscillation as it moves along the +x direction. A graph of the nanotube position as a function of time is shown here: http://dept.physics.upenn.edu/~robertjo/gmx/nt-position.jpg What is causing oscillations of this type? I was expecting the nanotube to move at a constant rate. Does this have anything to do with the fact that I'm pulling the nanotube in vacuum? Perhaps in aqueous solution, the solvent will damp these types of oscillations. Any ideas as to how to remove this? Thanks, Bob _______________________________________________ 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
