Could anyone please explain the difference between how "umbrella" and "constaint" options in the pulling code work. Based on the manual, I expect that the only difference is that umbrella used harmonic potential to bind pulled group to the reference group (point), while "constraint" uses shake algorithm to rigidly bind the groups. However, the simulations shows that this is not true. With all other options being the same, umbrella provides expected pulling, while constraint exhibits rather fluctuations of the pulled group nearby starting position. What do I miss?
Dr. Vitaly V. Chaban output from the "constraint" simulation with moving reference point (i.e. pull_geometry = position) z-coordinate 6.38675 5.97254 5.88948 5.86992 5.72523 5.59002 5.84313 5.83232 5.88722 5.83665 6.00198 5.96873 5.57108 5.35213 5.47916 5.46968 5.40241 5.41725 5.4732 5.45464 5.61582 5.66366 5.8005 5.9086 6.10943 6.11296 6.21684 5.95532 5.89226 6.00983 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
