Hi Gavin, A question arose for me: why did you consider the (rate = 0)?
Dariush On Fri, Jan 6, 2012 at 11:47 AM, Gavin Melaugh <gmelaug...@qub.ac.uk> wrote: > 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 > -- Kind Regards, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501 Fifth Avenue Pittsburgh, PA 15261 USA
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