Hi Thomas Many Thanks for the reply. I have attached the histograms I get for the umbrella sampling. My concern is the black histogram in which I have set the ref dist to be zero. The distances in the first few windows are very small as I really wanted this difficult region to be sampled well and therefore there might be some sampling in the negative distances. Does the picture here fit with your explanation below ?
Cheers Gavin Thomas Schlesier wrote: > I think that for the histogram all contribution with a negative sign > would be add to the contributions from positive distances. If your > distribution is be a perfect gaussian with zero mean, you would end up > with half a gaussian with double high (for positive distances) and > zero for negative distances. For this case it would be easy to correct > the histogram. But if the histogram isn't a perfect gaussian, you > couldn't say anything. > > > >> Date: Tue, 10 Jan 2012 10:47:43 +0000 >> From: Gavin Melaugh<gmelaug...@qub.ac.uk> >> Subject: Re: [gmx-users] RDF(PMF) and Umbrella sampling >> To: Discussion list for GROMACS users<gmx-users@gromacs.org> >> Message-ID:<4f0c174f.2050...@qub.ac.uk> >> Content-Type: text/plain; charset=ISO-8859-1 >> >> Hi Justin >> >> Again, many thanks for the reply. >> So when the COM distance changes sign, what effect does that have on the >> distribution of the COM distance about the mean value for that window >> i.e. If say my ref dist in 0 nm and the umbrella sampling allows the >> distance to sample distances say at 0.02 nm to -0.02nm. What happens to >> negative values? Obviously they are not counted as negative in the >> distribution or else it would be centred at zero/ >> >> Cheers >> >> Gavin >> >> Justin A. Lemkul wrote: >>> >>> >>> Gavin Melaugh wrote: >>>> Hi Justin >>>> >>>> Thanks very much. One last question. What do you mean when you say >>>> "COM >>>> reference distance is changing signs"? I thought the COM distance was >>>> the absolute distance between the two groups and therefore cannot be >>>> negative? >>>> >>> >>> The pull code deals in vectors. Signs can change. The use of >>> "distance" as a geometry is perhaps somewhat misleading. >>> >>> -Justin >>> >>>> Cheers >>>> >>>> Gavin >>>> >>>> Dariush Mohammadyani wrote: >>>>> 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 >>>>> <mailto: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 >>>>> <mailto: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 >>>>> <mailto: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 >>>>> >>>> >>> >> >> >> >> ------------------------------ >> >> Message: 3 >> Date: Tue, 10 Jan 2012 10:54:19 +0000 >> From: Steven Neumann<s.neuman...@gmail.com> >> Subject: [gmx-users] Energy Minimization >> To: Discussion list for GROMACS users<gmx-users@gromacs.org> >> Message-ID: >> <cakzjqqgcxr6pqjemepfjivu8+y_qn3bgmqm6jf3wksk48uv...@mail.gmail.com> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Dear Gmx Users, >> >> I am setting up my simulations of carbon tube with protein. I >> solvated my >> system, added ions and I would like to run EM of my system. My >> carbons of >> the tube in MD will be restrained. In this case should I run EM of my >> protein in water (and with ions) separately and the copy coordinates and >> then process with NVT and NPT or run EM with restrained nanotubes of my >> system directly? >> >> Thank you, >> >> Steven >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://lists.gromacs.org/pipermail/gmx-users/attachments/20120110/46237a45/attachment-0001.html >> >> >> ------------------------------ >> >
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