Hi Justin Thanks for the reply. I wanted my "pulling" to be free in all directions, that is in the liquid state with no defined reaction coordinate i.e not along a specific axis. This is why I used geometry = distance. Would you agree with this approach? By free I mean. The absolute distance between the COG of the ref group and that of the pull group.
Cheers Gavin Justin A. Lemkul wrote: > > > Gavin Melaugh wrote: >> Dear all >> >> I have a query regarding umbrella sampling simulations that I have >> carried out to study a dynamical process of a guest inserting into a >> host. I always get get a wall tending off to infinity at or just before >> the zero distance between the >> two species. >> The process I describe, for one system in particular, happens readily >> and I have compared the PMF from a non constrained simulation (via the >> RDF and reversible work theorem) and the same PMF from a set of >> umbrella sampling >> simulations. They agree quite well but in the non constrained simulation >> I get a minimum practically at zero whereas for the umbrella sampling >> the minimum is shifted and there is an infinite wall close to zero. This >> wall is not present from the reversible work theorem. Why the infinite >> wall? Why does the black histogram not centre around zero. Is this an >> artefact of the umbrella technique? Please see attached the profile from >> the umbrella sampling technique, and the corresponding histograms. >> > > What's happening is the COM reference distance is changing signs, so > you get an artifact. The "distance" geometry is relatively inflexible > and is only suitable for straight pulls of continuously increasing or > continuously decreasing COM distance. You should try using the > "position" geometry instead. There are some notes that you may find > useful in my tutorial: > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05a_pull_tips.html > > > -Justin > >> Here is an excerpt from one of the umbrella mdp files. >> >> pull = umbrella >> pull_geometry = distance >> pull_dim = Y Y Y >> pull_start = no >> pull_ngroups = 1 >> pull_group0 = cage_1 >> pull_group1 = tail >> pull_init1 = 0 >> pull_rate1 = 0.0 >> pull_k1 = 10000 >> pull_nstxout = 150 >> pull_nstfout = 150 >> >> >> Cheers >> >> Gavin >> >> >> ------------------------------------------------------------------------ >> >> >> ------------------------------------------------------------------------ >> > -- 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
