Hi Justin Just a quick clarification regarding my previous point. With geometry = distance, and pull_dim =Y Y Y . Is the pull_group sampling all dimensions equally (or without prejudice) about pull_init ? And iN your first reply what did you mean about by "straight pull" ?
Cheers Gavin Justin A. Lemkul wrote: > > > Gavin Melaugh wrote: >> 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? > > I suppose there is an argument that can be made for a more free > approach such as this one, but you're going to get the artifact you > observed the instant your pull group moves past a zero COM distance. > Whether or not this is a significant problem is something you'll have > to determine. > > -Justin > >> 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
