On Fri, Aug 31, 2012 at 1:45 PM, Steinbrecher, Thomas (IPC) <thomas.steinbrec...@kit.edu> wrote: > However, when I make the following two changes in my input file: > > pull_start = no > pull_init1 = 1.95 > > which should (?) amount to an equivalent setup, a very different trajectory > results in which the COM distance quickly increases to 2.7 nm and then > appears to be restrained there. (Visualization confirms, in the first case, > the groups remain in their starting conformation, in the second one, they are > pushed appart)
My guess is that you should use -1.95 as pull_init1 (mind the minus sign) and that the COM distance you measure is actually close to 2.9 nm (which is 1.95*2). g_dist measures a distance which is always non-negative, however pull_init1 is used as a reference position so its sign depends on the geometry of pulling. Cheers, Bogdan -- 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
